User: cmdcolin

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cmdcolin510
Reputation:
510
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Trusted
Location:
United States
Website:
https://github.com/cmd...
Last seen:
14 hours ago
Joined:
4 years, 7 months ago
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Bioinformatics at MSU

Posts by cmdcolin

<prev • 109 results • page 1 of 11 • next >
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Answer: A: from GI or protein ID to genome coordinates
... To add onto the answer by @andrey.v.shubin I made a small script to try to query a large text file programmatically, if you have a file with a large list of protein IDs you can try and speed up NCBI queries like this #!/usr/bin/env bash while read l1; do read l2 read l3 ...
written 14 hours ago by cmdcolin510
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Generate syntenic blocks between two vertebrates
... If you want to get an idea of syntenic blocks between two vertebrates, what would be the best steps? For example, I have experimented with LASTZ but the aligned pieces are quite small, so a more coarse level overview of synteny is a goal. Should I post process the alignments that LASTZ did using ch ...
alignment lastz synteny written 9 days ago by cmdcolin510 • updated 7 days ago by wangdp12350
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Comment: C: How To Convert Blast Results To Gff
... Updated again :) http://bergmanlab.genetics.uga.edu/?p=41 ...
written 10 days ago by cmdcolin510
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Comment: C: from GI or protein ID to genome coordinates
... Wondering what would be a good idea to do this on a mass scale, like all proteins in a genome? ...
written 14 days ago by cmdcolin510
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Comment: C: How to filter huge VCF files for datamining?
... Are you creating so-called gVCF files (I think this is what @lh3 referred to above)? It just doesn't seem like a normal VCF can conceivably have that much data. Also, have you considered doing joint genotyping? ...
written 14 days ago by cmdcolin510
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Comment: C: show vcf data in a table
... Note that VCF is already a table format (tsv) when it's uncompressed so you may not necessarily need to convert it to csv for example. Since the file is so large, you might take a subset of it to view. For example, if you are on linux you can get a small sample of the file using something like `gun ...
written 15 days ago by cmdcolin510
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Comment: C: Speeding up NUCmer for de novo contig to reference alignment
... just to improve google-ability of this page, the paper, in question here is "E-MEM: efficient computation of maximal exact matches for very large genomes " ...
written 15 days ago by cmdcolin510
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Comment: C: Looking for a bam file with aligned (error corrected) PacBio reads
... Links for bergman lab updated http://bergmanlab.genetics.uga.edu/?p=2176 http://bergmanlab.genetics.uga.edu/data/tracks/dm3/dm3PacBio.bam ...
written 15 days ago by cmdcolin510
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Answer: A: How To Retrieve Genbank Records With Range Of Accession Numbers
... You can use ncbi edirect tools (`brew install homebrew/science/edirect`) and run something like cat file_with_ids.txt | while read p; do echo $p; esearch -db nucleotide -query $p | efetch -format fasta > $p.fasta; done; or more simple cat file_with_ids.txt | while read p; do echo $p; ...
written 16 days ago by cmdcolin510
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Comment: C: How to filter huge VCF files for datamining?
... I am also surprised here, even 88 multiplied times the size of the human genome does not equal 4TB ...
written 19 days ago by cmdcolin510

Latest awards to cmdcolin

Scholar 7 days ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 14 days ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 21 days ago, created 100 posts.
Appreciated 5 weeks ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 5 months ago, voted more than 100 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.5 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 2.5 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Supporter 2.7 years ago, voted at least 25 times.
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