Subsampling aligned SAM/BAM files for RNA-seq analysis

Question

[mohammedtoufiq91]

Hi,

I would like to know if there are any specific tools to sub-sample aligned SAM or BAM files. What type of files could be considered for the sub-sampling sorted or unsorted SAM or BAM files.

Thank you, Toufiq

Answer 1

[WouterDeCoster]

You did not tell us anything about the aim of your analysis, which is probably important. For expression analysis I'd recommend subsampling the read counts. That is probably more efficient than subsampling alignments. First package that comes to mind is this R package: subseq

[mohammedtoufiq91]

We have generated a set of RNA-seq samples. These are human PE samples with read length of 150bp. We would like to identify the total number of genes that could be detected by reducing the number of reads to 1/2, 1/3rd and 1/4th. After this, identify the differentially expressed genes between the two conditions i.e. before/after treatment.

[ivivek_ngs]

There is a historical post. Check it out here.