search

epi2me-labs / wf-transcriptomes

Other
64 stars 30 forks source link

The mapping step statistics #73

Closed CHENAO-QIAN closed 1 month ago

CHENAO-QIAN commented 3 months ago

Ask away!

Hi,

I am trying to understand the final report. I saw two tables with alignment statistics — one is called read mapping summary, in which the numbers are much lower than expected; the other is alignment summary stats (in DE section), in which the numbers are closer to what I expect. IMG_5231

IMG_5230

I am confused:

  1. What are the differences between the two tables?
  2. Where are the numbers from? I got the same numbers as in the first table using samtools on sorted.bam, but could not figure out how to get the numbers from the second table.
sarahjeeeze commented 3 months ago

Hi, the first table is from alignment of each sample with the reference genome. The second table is alignment of each sample with the full non redundant transcriptome that is generated from the first part of the workflow which is why there are far more alignments - this info is then used to generate the counts for the DE analysis. Thanks for the feedback we will try to add explanations to these tables within the report in the future.

CHENAO-QIAN commented 3 months ago

Thank you for replying, Sarah!

I managed to regenerate the first table using bam files generated by the workflow. Does the workflow also have an intermediate file which I can use to generate the second table?

sarahjeeeze commented 1 month ago

Hey, no currently we aren't outputting that table as a file but in the near future you should be able to export this table from the report.