search

mozack / vdjer

V'DJer - B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data
Other
28 stars 5 forks source link

Few alignments output #16

Closed andrewjmc closed 5 years ago

andrewjmc commented 5 years ago

Hello,

I am testing VDJer on a transcriptomic sample. I aligned sequences with STAR (obtaining median read depth of the IGH region of 178, and up to 3000).

I was surprised to only get 52 alignments in the standard SAM file and 120 in sensitive mode.

Is this to be expected given the read coverage? I would be very grateful for your advice and can share further details as required.

Thanks!

mozack commented 5 years ago

Hi, A few factors can impact these results.

In order to assemble a contig in standard mode, we start to see good results at depth 50 - for a specific clone. So, if there are many clones expressed at low levels for example, V'DJer may not identify these.

Also, the read mapping to the assembled contigs requires exact matching. So, if you are working with error prone reads, you may wind up with a low alignment rate.

andrewjmc commented 5 years ago

Thanks!