I am looking for insertions 2-6 bp in length in the native novoalign output - but see that novoalign did not output any insertions greater than 1 bp. Am I looking for this wrong?
awk '$14 ~ /\+([AGTC]){2,}/ { print $0}'
None found
awk '$14 ~ /\+([AGTC])/ { print $0}'
Lots found
these are the changed parameters used in novoalign with 50 bp single end illumina reads:
-p '-F ILMFQ -t60 -r0.2 -q5' -l -w 24 -k 1 -t -o kaplan-em
am I missing them with these parameters?
thanks for any input!
awk '$14 ~ /\+([AGTC]){2,}/ { print $0}'
None found
awk '$14 ~ /\+([AGTC])/ { print $0}'
Lots found
these are the changed parameters used in novoalign with 50 bp single end illumina reads:
-p '-F ILMFQ -t60 -r0.2 -q5' -l -w 24 -k 1 -t -o kaplan-em
am I missing them with these parameters?
thanks for any input!
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