RNASEQR can not generate anchor sequences
Hi Guys,
I wonder any of you started to look into the package RNASEQR that claims to be the best of all RNA-Seq packages (who knows!). http://nar.oxfordjournals.org/conten...r.gkr1248.full
Does anyone have their old test sample set link? If so, I will appreciate the help. Basically, I used their test sample, but can not get any anchors generated while running the generate_anchors.py
script (phase2.anchors.fastq file has no reads), although the
phase2.sam input file looks fine.
It looks like the awk command does not return anything:
awk '^[^Q]/if { rshift($2, 2) %2==1) {print $1; print$10;$print11;}} phase2.sam
neither the loop for line in ps1:....was called.
What is this awk command trying to do?
I wonder any of you started to look into the package RNASEQR that claims to be the best of all RNA-Seq packages (who knows!). http://nar.oxfordjournals.org/conten...r.gkr1248.full
Does anyone have their old test sample set link? If so, I will appreciate the help. Basically, I used their test sample, but can not get any anchors generated while running the generate_anchors.py
script (phase2.anchors.fastq file has no reads), although the
phase2.sam input file looks fine.
It looks like the awk command does not return anything:
awk '^[^Q]/if { rshift($2, 2) %2==1) {print $1; print$10;$print11;}} phase2.sam
neither the loop for line in ps1:....was called.
What is this awk command trying to do?
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