Question: Question from student
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gravatar for rr14049
9 weeks ago by
rr140490
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 • 87 views
ADD COMMENTlink modified 9 weeks ago by Jennifer Hillman Jackson22k • written 9 weeks ago by rr140490
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gravatar for Jennifer Hillman Jackson
9 weeks ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

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 9 weeks ago by Jennifer Hillman Jackson22k
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