Question: Question from student
gravatar for rr14049
18 months ago by
United Kingdom
rr140490 wrote:

Hi all,

Does anyone know if it's possible to see the total number of raw reads, the number of reads mapped and the number of genes from a BAM file of mRNA-Seq data? Many thanks

Best Regards

rna-seq bam • 355 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 18 months ago by rr140490
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Basic summary stats after mapping can be found in one of these places:

  • A distinct output file (Tophat)
  • Under the "i" icon's "Job Details" page for the mapping run (HISAT, Bowtie)
    • Look under the stderr link on that page, but also check stdout

Try the tool htseq-count to compute sequence-per-gene counts from BAM files.

There are other methods but these are the most direct that I know of.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour