User: olechnwin

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olechnwin0
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Posts by olechnwin

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... Anybody knows whether any of these tools can be used to convert hg19 to a denovo genome assembled coordinate? ...
written 7 days ago by olechnwin0
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Comment: C: Visualize VarScan2 Copy Number Aberrations in IGV
... I don't think size is the problem. IGV supports SEG file and in their example.seq some of the segment is >15Mbp [SEG file format][1]. I tried to modify the cbs file generated by varScan to match their example.seq file but it just doesn't display the same way... [1]: https://software.broadinst ...
written 5 weeks ago by olechnwin0
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Comment: C: Visualize VarScan2 Copy Number Aberrations in IGV
... Hi Plum, Did you ever figure out how to do this? I'm trying to do the same. Thanks! ...
written 5 weeks ago by olechnwin0
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Comment: C: Annotation pipelines in 2018
... Does this mean if you intend to make the genome public you can request NCBI to do the annotation? ...
written 8 weeks ago by olechnwin0
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Comment: C: how to use faSplit to split fasta into x files
... hmm....thanks for the hint about checking the files I did `faSplit about` when I realized `faSplit sequence` does not work. But, upon checking the result, it seems that although `faSplit about` seems to be working properly, it didn't! **Update**: made a mistake. Seems to be working. At least for t ...
written 4 months ago by olechnwin0
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Comment: C: how to use faSplit to split fasta into x files
... Yes. I removed the test folder before running the faSplit with sed. My 1SQ_reads.fasta file is about 40 GB. ...
written 4 months ago by olechnwin0
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Comment: C: how to use faSplit to split fasta into x files
... This doesn't work either: $ ~/opt/miniconda3/bin/faSplit sequence <(sed 's#/#__#g' 1SQ_reads.fasta) 2 test/test_ $ ls test/test_* |wc -l 17188 ...
written 4 months ago by olechnwin0
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Comment: C: how to use faSplit to split fasta into x files
... @[RamRS][1], I tried to use your fasta file and it worked! $~/opt/miniconda3/bin/faSplit sequence seq.fa 2 test2/ $ ls test2/ 0.fa 1.fa $ ~/opt/miniconda3/bin/faSplit sequence seq.fa 3 test2/ $ ls test2/ 0.fa 1.fa 2.fa So, my FASTA identifiers are messing with the progra ...
written 4 months ago by olechnwin0
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Comment: C: how to use faSplit to split fasta into x files
... $ uname -a Linux qmaster01.cluster 2.6.32-696.30.1.el6.x86_64 #1 SMP Tue May 22 03:28:18 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux ...
written 4 months ago by olechnwin0
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Comment: C: how to use faSplit to split fasta into x files
... The faSplit binary does not work for me since it was built on a more recent OS than the one I currently has. ...
written 4 months ago by olechnwin0

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Popular Question 11 months ago, created a question with more than 1,000 views. For macs2: how to retrieve normalized counts

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