> 
> Dear Simon,
> I am using HT-Seq count to obtain counts on sorted bam files based on gene-id as you recommended, but I had a problem.
> 
> I started by using the GTF file from UCSC ensemble genes (build 72), which seemed to work fine and produced a file of counts per bam file. However I realised looking at one of our genes of interest, which "had" to be expressed, that the counts were 0. 
> 
> By looking at the bam files with IGV it shouldn't because a good number of reads were mapped to exons of the gene. So I inspected the GTF and surfing BioC I found the issue of gene_id being equal to transcript_id in Ensembl_UCSC gtfs, and I remembered you advised us to use the one from Ensembl ftp, hence, If I understood well the error, that meant we were counting only genes with just one transcript, hence all the others, ht-seq count (-m union -t exon) with overlapping exons, were losing those reads, or at least they were given only the reads of the "unique" exons. Indeed, the histogram looked very left shifted with most of the features with a mean (in 9 samples, 3 groups) less than 10.
> 
> Then I downloaded the new GTF from Ensembl, and I encountered the second problem. Again discussed in the past here and elsewhere about chromosome names not beginning with 'chr'. I applied the line: 
> 
> awk '{print "chr"$0}' Homo_sapiens.GRCh37.72.gtf | sed 's/chrMT/chrM/g' > hg19.ensembl-with-chr.gtf
> 
> ..that I found in the internet. Checked again the GTF, and sent the htseq-count.py with this command, as usual:
> 
> /usr/local/cluster/bin/samtools view $bamFile | /usr/local/cluster/python2.7/bin/python2.7 /usr/local/cluster/python2.7/bin/htseq-count -m union -t exon -s no -q - $GTF > $out
> 
> Got again the counts. When looked at the histogram with DESeq2 doing:
> 
> hist(log2(assay(ddsFull)),breaks=50)
> 
> ..the histogram had shifted right, meaning that I was including now many more counts in genes by avoiding the gene_id=transcript_id_many_ambiguous_issue.
> Then I checked again my favourite gene, but got 0 again!! and here is my puzzle.
> The bam file with IGV looks like this:
> 
> <Screen Shot 2013-07-17 at 11.26.58 AM.png>
> 
> I let you see the lines of my GTF coming from the ENSEMBL_GENE_ID of my gene, as downloaded from ftp of ensembl build 72 (genome used hg19, aligner SOAPSplice), after adding "chr":
> 
> chr19	protein_coding	exon	18263626	18264104	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003067609";
> chr19	protein_coding	exon	18266267	18267011	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003474719";
> chr19	protein_coding	CDS	18266690	18267011	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	start_codon	18266690	18266692	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001";
> chr19	protein_coding	exon	18271281	18271373	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "3"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003603229";
> chr19	protein_coding	CDS	18271281	18271373	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "3"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18271729	18271779	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "4"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003645468";
> chr19	protein_coding	CDS	18271729	18271779	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "4"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18271864	18271995	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "5"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003662245";
> chr19	protein_coding	CDS	18271864	18271995	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "5"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18272089	18272305	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "6"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003498230";
> chr19	protein_coding	CDS	18272089	18272305	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "6"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18272776	18272861	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "7"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003464305";
> chr19	protein_coding	CDS	18272776	18272861	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "7"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18273012	18273120	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "8"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003516250";
> chr19	protein_coding	CDS	18273012	18273120	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "8"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18273218	18273316	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "9"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003540261";
> chr19	protein_coding	CDS	18273218	18273316	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "9"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18273777	18273957	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "10"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003546729";
> chr19	protein_coding	CDS	18273777	18273957	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "10"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18274073	18274198	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "11"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003571819";
> chr19	protein_coding	CDS	18274073	18274198	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "11"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18276970	18277112	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "12"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003506088";
> chr19	protein_coding	CDS	18276970	18277112	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "12"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18277940	18278116	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "13"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003589841";
> chr19	protein_coding	CDS	18277940	18278116	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "13"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18279285	18279356	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "14"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003502685";
> chr19	protein_coding	CDS	18279285	18279356	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "14"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18279536	18279706	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "15"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00003498129";
> chr19	protein_coding	CDS	18279536	18279706	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "15"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	exon	18279897	18281350	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "16"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; exon_id "ENSE00000893034";
> chr19	protein_coding	CDS	18279897	18280101	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "16"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001"; protein_id "ENSP00000222254";
> chr19	protein_coding	stop_codon	18280102	18280104	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000222254"; exon_number "16"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-001";
> chr19	protein_coding	exon	18264092	18264418	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000473973"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-003"; exon_id "ENSE00001921962";
> chr19	protein_coding	exon	18266267	18266808	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000473973"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-003"; exon_id "ENSE00001834321";
> chr19	protein_coding	CDS	18266690	18266808	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000473973"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-003"; protein_id "ENSP00000470075";
> chr19	protein_coding	start_codon	18266690	18266692	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000473973"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-003";
> chr19	nonsense_mediated_decay	exon	18266432	18267011	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00001721882";
> chr19	nonsense_mediated_decay	CDS	18266690	18267011	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	start_codon	18266690	18266692	.	+	0gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002";
> chr19	nonsense_mediated_decay	exon	18271281	18271373	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003603229";
> chr19	nonsense_mediated_decay	CDS	18271281	18271373	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18271729	18271779	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "3"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003645468";
> chr19	nonsense_mediated_decay	CDS	18271729	18271779	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "3"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18271864	18271995	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "4"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003662245";
> chr19	nonsense_mediated_decay	CDS	18271864	18271995	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "4"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18272089	18272305	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "5"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003498230";
> chr19	nonsense_mediated_decay	CDS	18272089	18272305	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "5"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18272776	18272861	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "6"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003464305";
> chr19	nonsense_mediated_decay	CDS	18272776	18272861	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "6"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18273012	18273120	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "7"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003516250";
> chr19	nonsense_mediated_decay	CDS	18273012	18273120	.	+	2	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "7"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18273218	18273316	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "8"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003540261";
> chr19	nonsense_mediated_decay	CDS	18273218	18273316	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "8"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18273777	18273957	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "9"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003546729";
> chr19	nonsense_mediated_decay	CDS	18273777	18273957	.	+	1	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "9"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18274073	18274198	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "10"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003571819";
> chr19	nonsense_mediated_decay	CDS	18274073	18274198	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "10"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	exon	18276921	18277112	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "11"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00001646815";
> chr19	nonsense_mediated_decay	CDS	18276921	18276947	.	+	0	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "11"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; protein_id "ENSP00000395636";
> chr19	nonsense_mediated_decay	stop_codon	18276948	18276950	.	+	0gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "11"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002";
> chr19	nonsense_mediated_decay	exon	18277940	18278116	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "12"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003595850";
> chr19	nonsense_mediated_decay	exon	18279285	18279356	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "13"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003569756";
> chr19	nonsense_mediated_decay	exon	18279536	18279706	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "14"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00003638071";
> chr19	nonsense_mediated_decay	exon	18279897	18280883	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000426902"; exon_number "15"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-002"; exon_id "ENSE00001779641";
> chr19	retained_intron	exon	18271677	18271779	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000474310"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-004"; exon_id "ENSE00001888508";
> chr19	retained_intron	exon	18271864	18271995	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000474310"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-004"; exon_id "ENSE00003611107";
> chr19	retained_intron	exon	18272089	18272278	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000474310"; exon_number "3"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-004"; exon_id "ENSE00001872488";
> chr19	retained_intron	exon	18273004	18273120	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000600533"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-008"; exon_id "ENSE00003164217";
> chr19	retained_intron	exon	18273218	18273527	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000600533"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-008"; exon_id "ENSE00003205602";
> chr19	retained_intron	exon	18276966	18277112	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000464016"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-006"; exon_id "ENSE00001931248";
> chr19	retained_intron	exon	18277940	18278116	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000464016"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-006"; exon_id "ENSE00003595850";
> chr19	retained_intron	exon	18279285	18279706	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000464016"; exon_number "3"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-006"; exon_id "ENSE00001846742";
> chr19	retained_intron	exon	18279897	18279962	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000464016"; exon_number "4"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-006"; exon_id "ENSE00001924470";
> chr19	retained_intron	exon	18279228	18279356	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000459743"; exon_number "1"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-005"; exon_id "ENSE00001827706";
> chr19	retained_intron	exon	18279536	18279560	.	+	.	gene_id "ENSG00000105647"; transcript_id "ENST00000459743"; exon_number "2"; gene_name "PIK3R2"; gene_biotype "protein_coding"; transcript_name "PIK3R2-005"; exon_id "ENSE00001913624";
> 
> 
> 
>  What could be the problem? Thanks in advance
> Regards
> Jose
> 
> ------------------------------------------------------------
> Jose M. Garcia Manteiga PhD
> 
> Data analyst in Functional Genomics
> Center for Translational Genomics and Bioinformatics
> DIBIT2-A3 Room 21
> San Raffaele Scientific Institute
> Via Olgettina 58
> 20132 Milano
> Italy
> 
> Office: +39 02 26439114
> 
> 
> 
> 
> 
> 


	[[alternative HTML version deleted]]

