Moderator: swbarnes2
swbarnes2 ♦ 3.8k
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Posts by swbarnes2
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Answer:
A: Trim Paired-end Fastq Files
... Step one...ask the person who gave you the fatsq how they were filtered. The fastqs that came off the instrument should all be paired and in order. You might have fastqs where some reads were purged for quality reasons while their mates were left in the file. Or one was truncated. ...
written 1 day ago by
swbarnes2 ♦ 3.8k
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... Are you sure that your header order of chromosomes really is the same order as no-mouse.bam? ...
written 3 days ago by
swbarnes2 ♦ 3.8k
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... Nope. No special options, no post processing. Version 2.19 if I remember right. Indices are included in the undetermined fastq file, but not the sample fastqs.
Actually, I see that it depends on the instrument. I run the same version and command line of bcl2fastq on the Miseq, and I see indic ...
written 4 days ago by
swbarnes2 ♦ 3.8k
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... You are saying that you filtered away huge numbers of reads with -F 4 without disturbing the read 1 and read 2 pairing? -F 12 would probably work, I'm really surprised that Picard took all those orphan reads in stride. ...
written 4 days ago by
swbarnes2 ♦ 3.8k
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... I trust the sample sheet to have that information correct. ...
written 5 days ago by
swbarnes2 ♦ 3.8k
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... Shouldn't step one be to split out the piped parts into separate lines, so you at least know which command is at fault? Putting versions helps too...lots of people still using really old versions of samtools, ...
written 5 days ago by
swbarnes2 ♦ 3.8k
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... My fastqs have no barcodes in their header. (bcl2fastq v2.19.403) Only undetermined samples have that.
...
written 5 days ago by
swbarnes2 ♦ 3.8k
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... Why is this superior to just using the original fastqs? ...
written 5 days ago by
swbarnes2 ♦ 3.8k
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139
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... The read group is not the problem. The problem is that bwa expects the first read of file one to be the mate of the first read of file 2. That assumption obviously does not hold throughout the whole file, because sorting by coordinates and throwing away reads ruins that. ...
written 7 days ago by
swbarnes2 ♦ 3.8k
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... Aligning to see if the adapter is there will be slow. There might not be a way around that. It might be faster to use a regex to look for exact matches, and align only the ones that fail the perfect regex match.
Are you sure that there is no out of the box software that can do this for you? I'm ...
written 8 days ago by
swbarnes2 ♦ 3.8k
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