Moderator: John

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John11k
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Germany
Website:
http://at.cg/
Last seen:
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5 years, 5 months ago
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Mistakes will be made...

Posts by John

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Comment: C: Malformed BAM file produced by BWA
... The RG tag has to be added manually, so it's not really a "corrupt" BAM... you just haven't added RG metadata and GATK needs that. AddOrReplaceReadGroups is the answer. Why didn't it, er, "avail"? :) ...
written 7 hours ago by John11k
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Comment: C: GATK on RNASeq/ChIP data - distinction between no SNP and no data.
... It's been over a year and a half since i did this, so im afraid my advice will be a little outdated. Bottomline, the GATK RNASeq best practises leaved much to be desired 1.5yrs ago. Perhaps it's better now, but truthfully, you probably know more than i do on this matter if you've read the GATK docs ...
written 13 hours ago by John11k
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Comment: C: DNA fragmentation is biased
... Hm, very interesting... Perhaps take a look at the adipocyte DEEP samples, as these samples underwent almost all the steps of NEXSON (in that Laura sequenced them like all the other DEEP samples, and i sonicated the purified nuclei with something very close to Laura's sonication settings), but puri ...
written 1 day ago by John11k
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Comment: C: DNA fragmentation is biased
... About 3 years ago my lab had planned to do an experiment where DNA was sonicated in such a way that well-sonicated fragments (100-700bp) would be sequenced, and compared to poorly sonicated fragments (10kb+) that underwent an additional step of mild-decrosslinking and re-sonicated to get it to the 1 ...
written 1 day ago by John11k
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Answer: A: StackExchange/Area51 bioinformatics is back
... ![SKUB][1] There are 101 ways one could make a stronger, healthier bioinformatics community, but honestly whether you have nested comments or downvotes on the forum UI....... i just don't see it as a big deal. How many of us went into Bioinformatics because we're real particular about our user inte ...
written 3 days ago by John11k
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Comment: C: StackExchange/Area51 bioinformatics is back
... :D ...
written 3 days ago by John11k
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Comment: C: pybam - 100% python BAM reader
... I wish! :P But the update really was about cleaning it up for the thesis, doing proper tests, raise proper error messages, etc, so perhaps a small contribution to it :) I'll probably be (re)publishing 1 new program a week for the next few weeks, hehe ...
written 6 days ago by John11k
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Answer: A: pybam - 100% python BAM reader
... Pybam Beta is now done: https://github.com/JohnLonginotto/pybam It's just all-round better than the previous version in terms of how you use the API. Perhaps the two most interesting things are: 1. It can do dynamic and static parsing (decode something from BAM to SAM as and when you need it, ...
written 6 days ago by John11k
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Comment: C: It's about the journey, and not the destination
... I feel this is more of a blog than a tutorial... ...
written 16 days ago by John11k
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Answer: A: SAM to BAM conversion issues
... Maybe i've got it wrong, but don't you want to identify your special CCGG reads *after* removing adapters? If that's the case, i'd follow Devon's advice and just start over. Remap with a proper bisulphite mapper (I use BWA-meth, but i don't know if it works with 5hmC), do the QC trimming the Bisulp ...
written 16 days ago by John11k

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