search

itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
10 stars 5 forks source link

does sam2mappingstats.pl/getstats.pl handle single-end data? #8

Closed fossilfriend closed 10 years ago

fossilfriend commented 10 years ago

Totals mapped all reads as reverse instead of forward; but tallies did look correct. getstats.pl failed with a div by zero error.

eunjijunekim commented 10 years ago

I fixed the sam2mappingstats.pl script. it should report the reads as forward reads now. I didn't get any error from getstats.pl, but please let me know if it still fails after running the new sam2mappingstats.pl script.

fossilfriend commented 10 years ago

I reran runall_sam2mappingstats.pl and the read counts look good. So thanks for fixing that!

However, I still got a div by zero error from getstats.pl.

I added some debugging statements to the script to see if I could track down the problem.

I learned that for only one of my samples, the sample.mappingstats.txt file produced by sam2mappingstats.pl is empty. Unfortunately the associated error log was also empty and the standard out log implies that the Aligned.out.sam file was successfully processed. I reran sam2mappingstats.pl on this one sample thinking there was a chance the node had an issue writing to the file, but got the same result: no error but empty output. Not sure what is going on ... any ideas why this might happen?