User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey720
Reputation:
720
Status:
Trusted
Location:
Karimannoor
Last seen:
10 hours ago
Joined:
2 years, 4 months ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 96 results • page 1 of 10 • next >
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Comment: C: Bedtools intersect alternatives available
... John, Confirmed. With -sorted itself it is slow. Jeffin ...
written 13 hours ago by Jeffin Rockey720
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Comment: C: Bedtools intersect alternatives available
... Alex, Even without --faster bedops was significantly faster and that speedup itself was sufficient. But the difference in results of --element-of 1 from bedtools intersect is what held me back from using bedops. ...
written 1 day ago by Jeffin Rockey720
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Comment: C: Bedtools intersect alternatives available
... Thanks Alex. I shall try with the mentioned options and see if they can be used instead. ...
written 1 day ago by Jeffin Rockey720
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Comment: C: Bedtools intersect alternatives available
... John, I remember so. Let me cross check again. Shall confirm on this at the earliest. ...
written 1 day ago by Jeffin Rockey720
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Comment: C: Bedtools intersect alternatives available
... When I tried to ‎ parallelize bedtools, they are in fact individually slowing down effectively nullifying the expected advantage. I checked in different servers[256 GB], but this behaviour is recurring, may be something to do with RAM. ...
written 1 day ago by Jeffin Rockey720
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Comment: C: Bedtools intersect alternatives available
... There are 10+ methylome bedfiles which have the positions of methylated bases. They are obtained through bwa-meth followed by methyldackel followed by conversion to bed. Roughly each file has 80,000,000+ entries. I was trying to intersect these with gene features like exons. The count came as expect ...
written 1 day ago by Jeffin Rockey720
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Bedtools intersect alternatives available
... What are the alternative tools available which can do what `bedtools intersect` does? ...
bedtools written 1 day ago by Jeffin Rockey720 • updated 1 day ago by Alex Reynolds26k
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Comment: C: Error using bedtools "intersect" command
... Do sorting of both the files with sort -V giving appropriate columns (e.g,1-3 in the given file.bed) and then try . ...
written 2 days ago by Jeffin Rockey720
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Answer: C: ddRAD analysis pipelines
... Resolved now. The reason was completely unexpected. The enzyme cut-site sequence I provided was incorrect. So in filtering step most of the reads did not pass(zero for all most all samples). This caused the error downstream at step6. Once I gave the correct cut-site it worked as expected.Took ...
written 6 days ago by Jeffin Rockey720
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Answer: A: Error in cutadapt installation
... Would be easier through conda. Download and run https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh if 64 bit. Then exit and re-login for ~/.bashrc entries to take effect or run source ~/.bashrc instead. Then install cut adapt with command `conda install -c bioconda cutadapt` ( ...
written 9 days ago by Jeffin Rockey720

Latest awards to Jeffin Rockey

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Scholar 7 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 7 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 14 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 16 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 19 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 2.1 years ago, created an answer that has been accepted. For A: parsing through gtf file

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