User: manuel.belmadani
manuel.belmadani • 570
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Posts by manuel.belmadani
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... Would this take care of the simulation part?
http://bioinfo.ict.ac.cn/OpenMS-Simulator/
This might be useful for assembly, https://github.com/warrenlr/PASS some of the outputs look similar to the example you provided (with some differences, e.g. using sequence name instead of peptide in the first ...
written 3 days ago by
manuel.belmadani • 570
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... By the way, `chainsaw` from Proteowizard might be useful for digestion: http://proteowizard.sourceforge.net/tools/chainsaw.html ...
written 3 days ago by
manuel.belmadani • 570
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... I think paired-end reads would be guaranteed to be adjacent in a sort-by-name, whereas it wouldn't necessarily be so with a coordinate sorted BAM. ...
written 6 days ago by
manuel.belmadani • 570
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... cutadapt should get rid of reads > 30 in length in that case. Are you sure that you have the trimmed file in `my_files`, and not the original file you had before running cutadapt? ...
written 7 days ago by
manuel.belmadani • 570
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... Make sure; do `awk '{print length}' | sort -n | tail` . The last number should be the longest sequence length in your file. Remove the headers before if you think they're longer than 30bp (i.e. `grep -v ">" | awk '{print length}' | sort -n | tail` ...
written 7 days ago by
manuel.belmadani • 570
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... By the way, the `-f` switch in grep allows you to provide a file of patterns to search; e.g. `grep -f `, so possibly your could get rid of your inner for loop. ...
written 7 days ago by
manuel.belmadani • 570
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... It's complaining about `or die "Can't read from $infile: $!";`. Which makes sense, if `open (my $infile, "<", "namconvmars.txt")` fails for some reason, then `$infile` wont be set, so you can't use it in your error message (which would print the content of the file anyways, probably not what you ...
written 11 days ago by
manuel.belmadani • 570
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... I added the `>` in the character class. Just be careful that your FASTA files don't have reads over multiple lines, or it'll break (and add AAAAAA at each non-header begining of line, even if multiple lines are part of the same contiguous reads.) This use case is a bit more complicated than the p ...
written 11 days ago by
manuel.belmadani • 570
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... `sed` will do that:
$ sed 's|^[^@>]\(.*\)|AAAAAA\1|g' fastq.fq
@header
AAAAAATCTCAGATCGGAAGAGCACACGT
@header
AAAAAACGGTCCTGGTTGCAGATCGGAAG
@header
AAAAAATATCTCCTAAGATATAACAGGTTG
@header
AAAAAAGGTACAGGTTGGATGATAAGTCC
$ sed 's|^[^@>]\(.*\)|AAAAAA\1|g' f ...
written 12 days ago by
manuel.belmadani • 570
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... You want to split your input on space, not tab.
e.g.
# my @cols = split(/\t/); # Change this
my @cols = split(' '); # To this. ...
written 12 days ago by
manuel.belmadani • 570
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