Hello,

I'm trying to use featureCounts to extract read counts per transcript from
the SAM file (generated using Bowtie2) mapped to de novo assembled
transcripts (for DE analysis). I made annotation file as per the SAF
requirements:

Eg:

*GeneID Chr Start End Strand*
Locus_47_Transcript_16/31_Confidence_0.158_Length_1485
Locus_47_Transcript_16/31_Confidence_0.158_Length_1485 1 1485 +
Locus_58_Transcript_85/85_Confidence_0.017_Length_650
Locus_58_Transcript_85/85_Confidence_0.017_Length_650 1 650 +

Here I made both the GeneID and the Chr columns same with *Start* being 1
and *End* as the length of the transcript and the Strand as + for all
transcripts.

When I used the following code, it does nothing for a while and then R
crashes.

library(Rsubread)
counts <-
featureCounts(files="AssembledTranscriptome-LMcontrol1.sam",annot="AnnotRsubreadSAF.txt",isGTFAnnotationFile=FALSE)

Rsubread works great with GTF as annot parameter on genome mapped SAM files
but not with the SAF, as I tried here.

 Please let me know where I'm wrong here or if anyone tried other packages
that serves the purpose.

sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C
          LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] Rsamtools_1.12.3                    edgeR_3.2.4
  Rsubread_1.10.5
 [4] ChIPpeakAnno_2.8.0                  GenomicFeatures_1.12.3
 limma_3.16.7
 [7] org.Hs.eg.db_2.9.0                  GO.db_2.9.0
  RSQLite_0.11.4
[10] DBI_0.2-7                           AnnotationDbi_1.22.6
 BSgenome.Ecoli.NCBI.20080805_1.3.17
[13] BSgenome_1.28.0                     GenomicRanges_1.12.4
 Biostrings_2.28.0
[16] IRanges_1.18.2                      multtest_2.16.0
  Biobase_2.20.1
[19] biomaRt_2.16.0                      BiocGenerics_0.6.0
 VennDiagram_1.6.4
[22] sendmailR_1.1-2                     base64enc_0.1-1
  BiocInstaller_1.10.3

loaded via a namespace (and not attached):
[1] bitops_1.0-5       MASS_7.3-26        RCurl_1.95-4.1
rtracklayer_1.20.4 stats4_3.0.1
[6] survival_2.37-4    tools_3.0.1        XML_3.98-1.1       zlibbioc_1.6.0

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