Entering edit mode
6.2 years ago
Katon
•
0
Hi All,
Recently I am working on a fruit fly RNAseq project. After indexing and mapping with STAR, now I need to calculate the number of uniquely mapped and annotated reads as well as the number of uniquely mapped but unannotated reads in the bam file.
Does anyone know whether bedtools or other tools could be used to solve this problem?
Thanks in advance!
Those are going to require
bedtools/bedops
.From STAR counts file, I think the N_noFeature is what he wants (
head -n 4 sample1.ReadsPerGene.out.tab
):P.S:: the three counts columns correspond to unstranded, 1st read strand aligned with RNA (htseq-count option
-s yes
), and 2nd read strand aligned with RNA (htseq-count option-s reverse
).Thank you soooo much for your help!! I have reprocessed the STAR with quantMode and got the tab file. Just curious, could we also get the number of genes from coding/non coding regions respectively by dealing with these output data?
Thanks again!
Thank you for your suggestion! It seems bedtools need two files to do comparison. Since I have already have an A file. Do you have any idea how to build an annotated gene B file based on those fasta and GTF files?
Thanks again!