This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Subsampling aligned SAM/BAM files for RNA-seq analysis

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

rna-seq subsampling downsampling sam bam
• 2,308 views • link
updated by WouterDeCoster WouterDeCoster • written by mohammedtoufiq91 mohammedtoufiq91

1 answer

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

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.

• 0 views • link
written by mohammedtoufiq91 mohammedtoufiq91

There is a historical post. Check it out here.

• 0 views • link
written by ivivek_ngs ivivek_ngs

Log in to answer this question.

More posts like this