Moderator: Ram

gravatar for Ram
Ram12k
Reputation:
12,380
Status:
Trusted
Location:
New York
Twitter:
@_RamRS
Scholar ID:
Google Scholar Page
Last seen:
43 minutes ago
Joined:
4 years, 4 months ago
Email:
r****@nyu.edu

Bioinformatician turned Microsoft technologies developer turned bioinformatician. I love messing with text. UNIX>R>Python>Perl programmer, Excel pro, master Googler, database expert. 

I'm an amateur biologist interested in translational human genetics and healthcare.

Twitter: @_ramrs

Posts by Ram

<prev • 2,640 results • page 1 of 264 • next >
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Comment: C: Trouble indexing a .vcf.gz file
... Thank you - I had no idea you could recompile bgzip with larger offsets (? pointer sizes maybe?). Good going! ...
written 1 day ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... I hope OP has access to good computing resources. In the meantime, I'd recommend using `bgzip -c` instead of plain `bgzip`. ...
written 1 day ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... I guess that should be OK. I would change the headers too, but this thread says it might not be necessary: https://www.biostars.org/p/98582/ I'd still change it though, just because I like to play it consistent. ...
written 1 day ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... md5sum on a 37G VCF file shouldn't be cumbersome, just takes a while. ...
written 1 day ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... I second this - I do not trust parallel combinations with gzip or bgzip. I hope you retain the original file (the "old vcf file" that cpad mentions), OP. If bgzip did something funky, you're gonna need that file to restart your processing. ...
written 1 day ago by Ram12k
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Comment: C: htseq-count error on galaxy
... Hello costarc! We believe that this post does not fit the main topic of this site. Please ask https://biostar.usegalaxy.org/ For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why ...
written 1 day ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... Also, you say you added chromosome prefixes. Are you sure you added them everywhere, including the `##contig` lines and in all VCF entries? ...
written 2 days ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... Try `zcat file.vcf.gz | less -S` and eyeball it to check if everything looks OK. Just for starters. ...
written 2 days ago by Ram12k
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Comment: C: Trouble indexing a .vcf.gz file
... Please take some time and use the formatting bar (especially the `code` option) to present your post better. ![Formatting bar][1] [1]: https://preview.ibb.co/bDB1ub/vwl8c79mitb1n1o_preserve_transparency_False_size_1024x1024_size_mode_2.png ...
written 2 days ago by Ram12k
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Comment: C: bowtie text file on R
... OP, you're looking to read a text file hosted online in R. That is pushing the boundaries of the topics we discuss here, but I will open your question. Please elaborate on what your problem is and what you've tried the next time. For example, you've mentioned only one function you tried - that comes ...
written 3 days ago by Ram12k

Latest awards to Ram

Scholar 6 days ago, created an answer that has been accepted. For A: BCFtools variant calling format
Appreciated 21 days ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Scholar 26 days ago, created an answer that has been accepted. For A: BCFtools variant calling format
Scholar 28 days ago, created an answer that has been accepted. For A: Recompile bedops with increased TOKENS_MAX_LENGTH
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: bash loop for alignment RNA-seq data
Scholar 6 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Appreciated 6 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Appreciated 6 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Scholar 6 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Scholar 7 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Appreciated 9 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: bash loop for alignment RNA-seq data
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Scholar 10 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Appreciated 10 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)

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