Moderator: genomax2

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genomax224k
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Posts by genomax2

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Comment: C: Remove specific reads from fastq file
... BBMap should auto-detect the quality encoding format but if it does not be sure to add `qin=64` since this is old solexa format data (ref the link from WikiPedia above). You can also change the format of the Q-scores to more recent Illumina/sanger format by using `qout=33` when you use `reformat.sh` ...
written 2 hours ago by genomax224k
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Comment: C: Malformed VCF file at approximately line number 101449: The VCF specification d
... Please use `ADD COMMENT/ADD REPLY` when responding to existing posts to keep threads logically organized. ...
written 3 hours ago by genomax224k
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Comment: C: Remove specific reads from fastq file
... > @SRR066153.1 SOLEXA-1GA-2_1:1:1:0:715 length=36 > > This zero indicates the quality and I can somehow remove reads with > this quality? Don't think that is correct. Check the [Illumina fastq header format][1]. `SRR066153.1 ` bit comes from `fastq-dump`'ing the reads from SRA without ...
written 3 hours ago by genomax224k
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Answer: A: Remove specific reads from fastq file
... You can use `reformat.sh` from [BBMap suite][1] with the `maxns=` option (If 0 or greater, reads with more Ns than this (after trimming) will be discarded). [1]: https://sourceforge.net/projects/bbmap/ ...
written 3 hours ago by genomax224k
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Comment: C: filtering out reads from bam file
... You could convert your gff3 file to BED and then use `samtools view` region: https://www.biostars.org/p/97953/ ...
written 3 hours ago by genomax224k
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Comment: C: script to Extract longest isoform from stringTie assembly
... Please search Biostars (using a google search). It will save you having to ask these types of questions: https://www.biostars.org/p/107759/ ...
written 15 hours ago by genomax224k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Making an executable (not sure what OS's it can run on) will actually make it more accessible. ...
written 16 hours ago by genomax224k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... That would be the perfect alternative. You can also make the original code available on the side for those who are lucky enough to have access to Matlab licenses. You would not have to re-implement/re-code the software again. ...
written 16 hours ago by genomax224k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Any code which `requires` non-free software is going to limit accessibility/use by wider audience. Matlab would qualify for that. ...
written 19 hours ago by genomax224k
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Comment: C: Advice on best freeware to assemble a short 'toy' sequence from 18 very short un
... You could give `tadpole.sh` from [BBMap suite][1] a try instead of `SPAdes`. Note: Did you just make a new account to post this question under a different name? [1]: http://seqanswers.com/forums/showthread.php?t=61445 ...
written 20 hours ago by genomax224k

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