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Old 10-29-2012, 02:06 AM   #3
HenrivdGeest
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Location: Arnhem

Join Date: Feb 2012
Posts: 16
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Hello,

I just tried LSC, and it looks good;
some remarks:

-input cant be fastq, at first I tried to run with fastq but run into weird errors and crashes.
- It cant handle multiline fasta for pacbio long reads?
- documentation:
"full_LR_SR.map.fa
Although the terminus sequences are corrected, they are concatenated with their corrected sequence (corrected_LR_SR.map.fa) to be a "full" sequence. Thus, this sequence covers the equivalent length as the raw read and is outputted in the file full_LR_SR.map.fa"
I think this should be:
"Although the terminus sequences are uncorrected..."

- I dont understand this option:
" Remove PacBio tails sub reads?"

I use filtered pacbio subreads as input, and the fastq header "...s1_p0/16/3441_3479" means that this subread originates from the raw read at position 3441-3479 and is 38bp long. These tails are already removed by secondary filtering? (these tails might ended up in another subread)
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