[BioC] how to get the exon count by using htseq-count

[Hu Fuyan [guest]]

Dear teacher,
How to get the exon count by using htseq-count?
My script is:
python -m HTSeq.scripts.count -m intersection-strict --stranded=no -t exon -i exon_id  accepted_hits_name.sorted.sam Homo_sapiens.GRCh37.70_new.gtf>outfile_htseqcount_exon

For example gene SLC25A13 has 18 exons, how can I get the counts for the 18 exons?

How can I get the result like this (coming from easyRNASeq):
"\"ENSG00000004864\"_1" 2
"\"ENSG00000004864\"_2" 4
"\"ENSG00000004864\"_3" 16
"\"ENSG00000004864\"_4" 3
"\"ENSG00000004864\"_5" 7
"\"ENSG00000004864\"_6" 8
"\"ENSG00000004864\"_7" 5
"\"ENSG00000004864\"_8" 4
"\"ENSG00000004864\"_9" 4
"\"ENSG00000004864\"_10" 1
"\"ENSG00000004864\"_11" 6
"\"ENSG00000004864\"_12" 4
"\"ENSG00000004864\"_13" 4
"\"ENSG00000004864\"_14" 6
"\"ENSG00000004864\"_15" 8
"\"ENSG00000004864\"_16" 5
"\"ENSG00000004864\"_17" 3
"\"ENSG00000004864\"_18" 25







Here is a part from my genes.gtf (human ensembl)

7	protein_coding	exon	95951254	95951405	.	-	.	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "1"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001"; exon_id "ENSE00001830180";
7	protein_coding	CDS	95951254	95951268	.	-	0	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "1"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001"; protein_id "ENSP00000265631";
7	protein_coding	start_codon	95951266	95951268	.	-	0	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "1"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001";
7	protein_coding	exon	95926210	95926263	.	-	.	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "2"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001"; exon_id "ENSE00003192771";
7	protein_coding	CDS	95926210	95926263	.	-	0	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "2"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001"; protein_id "ENSP00000265631";
7	protein_coding	exon	95906508	95906650	.	-	.	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "3"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001"; exon_id "ENSE00003069204";
7	protein_coding	CDS	95906508	95906650	.	-	0	 gene_id "ENSG00000004864"; transcript_id "ENST00000265631"; exon_number "3"; gene_name "SLC25A13"; gene_biotype "protein_coding"; transcript_name "SLC25A13-001"; protein_id "ENSP00000265631";
7	protein_coding	exon

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=C                     LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] easyRNASeq_1.4.2       ShortRead_1.16.4       latticeExtra_0.6-24
  [4] RColorBrewer_1.0-5     Rsamtools_1.10.2       DESeq_1.10.1
 [7] lattice_0.20-13        locfit_1.5-8           BSgenome_1.26.1
[10] GenomicRanges_1.10.7   Biostrings_2.26.3      IRanges_1.16.6
[13] edgeR_3.0.8            limma_3.14.4           biomaRt_2.14.0
 [16] Biobase_2.18.0         genomeIntervals_1.14.0 BiocGenerics_0.4.0
[19] intervals_0.13.3

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.5 bitops_1.0-5
 [4] DBI_0.2-5            genefilter_1.40.0    geneplotter_1.36.0
  [7] grid_2.15.2          hwriter_1.3          RCurl_1.95-3
[10] RSQLite_0.11.2       splines_2.15.2       stats4_2.15.2
[13] survival_2.37-4      XML_3.95-0.1         xtable_1.7-1
[16] zlibbioc_1.4.0

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