Moderator: John

gravatar for John
John10k
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Germany
Website:
http://at.cg/
Last seen:
10 hours ago
Joined:
5 years, 4 months ago
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m***********@gmail.com

Mistakes will be made...

Posts by John

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Answer: A: identification of adapters from fastq file.
... This question has come up a lot before, and the answer is basically "if you really have no idea what adapters were used, you're screwed", because we don't have any tools to identify custom adapter sequences yet. You can detect over-represented sequences, but this is really a different sort of proble ...
written 14 hours ago by John10k • updated 14 hours ago by WouterDeCoster14k
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Answer: A: What to use after Salmon
... Mmm, salmon and rice... sounds like the recipe for a good sushi. All you need now is a little wasabi: https://github.com/COMBINE-lab/wasabi And then you can use Sluth from the Kallisto guys to do the downstream stuff: http://pachterlab.github.io/sleuth/ There's also SalmonTools: https://github.c ...
written 15 hours ago by John10k
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Comment: C: Does jellyfish 2 support kmer size > 31
... Probably because they originally used 64bits per kmer, which can store up to 32 bases in 2bit (less one for whatever reason, probably to signal reverse complementation or variable-lengths). With an update, this man-made constraint was removed. ...
written 4 days ago by John10k
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Comment: C: getting the unmapped reads from BAM file
... No no, sorry I know this is confusing, it's confusing for everybody. It means that the total number of reads you have is 22806328 (passed QC), plus 4861610 (failed QC), which gives 27667938 alignments in total. 11326152 + 1905487 is the number of paired-end reads (for forward, but also for reverse) ...
written 6 days ago by John10k
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Comment: C: basic concepts behind --sjdbOverhang (STAR)
... Right well, if you really want to understand it, you can search the STAR source code for all mentions of sjdbOverhang with this: https://github.com/alexdobin/STAR/search?p=1&q=sjdboverhang&utf8=%E2%9C%93 I don't personally understand c++ (else I would have read it and answered the question ...
written 8 days ago by John10k
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Answer: A: basic concepts behind --sjdbOverhang (STAR)
... Why dont you try running STAR with --sjdbOverhang 49 and then repeat with --sjdbOverhang 100, and check the difference :) I'm not trying to be cute about it - I assume for reads <100bp that 100 will work fine as per your reasoning. However, that assumption assumes the STAR manual reflects realit ...
written 8 days ago by John10k
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Comment: C: What is the current price of a bioinfo group?
... This is like asking how much money does it take to set up a small competitive hospital, with no more than 3 doctors. ...
written 8 days ago by John10k
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Comment: C: getting the unmapped reads from BAM file
... The way these numbers are laid out, is that the alignments on the left of the + have passed QC, while the alignments on the right have failed. That is also true for the "total", which is just the total for those passed/failed QC. So it's (11326152 + 1905487) x2 == 26463278, but total is 22806328 + ...
written 9 days ago by John10k
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Comment: C: getting the unmapped reads from BAM file
... Ah, i see. I didn't know BWA-meth gave secondary alignments like that. hm. Well, just so you are aware, the best option is probably to also map to the wheat genome and then for each read check if it aligned to rust, wheat, both, or neither, to get a proper statistic for this sort of thing. Or perha ...
written 9 days ago by John10k
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Comment: C: getting the unmapped reads from BAM file
... Was this the output of BWA-meth? This is a very scary looking BAM file, that's for sure. If you could provide more information about the experiment/sequencing type, that could help a lot in diagnosing the best solution. ...
written 9 days ago by John10k

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