User: fishka

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fishka20
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Posts by fishka

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Comment: C: Should I keep or remove the alignment reads whose mate reads mapped to a differe
... I do not understand the question. You have good alignment rate but pairs are aligned discordantly. It means, that most likely, your alignment parameters are wrong. Run `samtools view ...bam | head` And `samtools view ...bam|grep...` for 10 IDs. From pair coordinates you will see distance between pai ...
written 8 weeks ago by fishka20
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Answer: A: Cufflinks installation error
... Hi, it is specified rather obviously [here][1] You run `./configure` with parameters `—prefix`, etc. But `make` and `make install` (possibly with `sudo`) without any parameters. [1]: https://github.com/cole-trapnell-lab/cufflinks ...
written 8 weeks ago by fishka20
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Answer: A: Should I keep or remove the alignment reads whose mate reads mapped to a differe
... Try to change insertion size parameter to 1000 bp, for example, and check alignment rate. And also it would be reasonable to check reads orientation. Most likely it will solve the problem. ...
written 8 weeks ago by fishka20
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Answer: A: samtools installation errors
... try make clean make sudo make install ...
written 8 weeks ago by fishka20
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Comment: C: Should I keep or remove the alignment reads whose mate reads mapped to a differe
... Not necessarily, pair-end and mate-pair are two different techniques. Your problem can be caused by library preparation, wrong aligner settings. Not sure about flagstat "different chr". If you check a pair of reads with the same ID, are they really mapped to two different chromosomes? If chromosome ...
written 8 weeks ago by fishka20
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Answer: A: samtools installation errors
... you have to add sudo `sudo make install` ...
written 8 weeks ago by fishka20

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