Open tgenahmet opened 7 years ago
@tgenahmet @awchrist @denriquez
The biggest difference is that Pegasus: 1) Uses a newer version of STAR 2) It enforces that the RNA BAM now have RG tags just like we do on DNA.
As far as I remember those are the only differences. There maybe some different run settings related
The rnaAlign script still has a bug that occurs when re-running it. This code did the trick (I used "git diff" so sorry about the formatting) for now:
index df9ec7c..4f483a1 100755 --- a/pegasus_rnaAlign.sh +++ b/pegasus_rnaAlign.sh @@ -198,7 +198,12 @@ do
if [[ -e $ownDir.starPass || -e $ownDir.starFail || -e $ownDir.starInQueue ]] ; then
echo "### STAR already done, failed or inQueue"
echo $configLine | cut -d= -f2 | cut -d, -f1
echo $configLine | cut -d= -f2 | cut -d, -f2
echo $configLine | cut -d= -f2 | cut -d, -f3
unset mergeArrayLet me know your thoughts. I haven't pushed yet.
Ugghhh! Github changed the format. Here is the code again:
if [[ -e $ownDir.starPass || -e $ownDir.starFail || -e $ownDir.starInQueue ]] ; then
echo "### STAR already done, failed or inQueue"
kitName=echo $configLine | cut -d= -f2 | cut -d, -f1
samName=echo $configLine | cut -d= -f2 | cut -d, -f2
assayID=echo $configLine | cut -d= -f2 | cut -d, -f3
unset mergeArray
count=0
skipGroup=0
continue
fi
The rnaAlign script has a bug (only matters when trying to re-run). Needs to be fixed. While trying to debug I also realized the code is way more complicated than it needs to be. rnaAlign script in medusa makes a lot more sense. My plan is to change pegasus-rnaAlign to be more like medusa-rnaAlign.
Here's the question: what are the differences in rnaAlign between medusa and pegasus that I may not be aware of?
@denriquez @awchrist @PedalheadPHX