User: Tom Koch

gravatar for Tom Koch
Tom Koch110
Reputation:
110
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Trusted
Location:
Pine Biotech, New Orleans, LA, USA
Website:
http://www.pine-biotec...
Twitter:
metadatabobeta
Last seen:
2 years, 9 months ago
Joined:
3 years, 10 months ago
Email:
t**@pine-biotech.com

Posts by Tom Koch

<prev • 13 results • page 1 of 2 • next >
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Forum: Omics Data Analysis and Bioinformatics in Education Survey
... Previously, Elia posted about a survey we'd designed in Bioinformatics Survey to help make bioinformatics useful!. The results of that survey were posted in full on the company blog, and now there is a new survey focused on Bioinformatics in Education, as well as the needs in Omics Data Analysis. T ...
forum chip-seq rna-seq sequencing written 2.8 years ago by Tom Koch110
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News: Pine Biotech releases two replication studies designed for bioinformatics educational use
... Project-based learning is one of the most successful methods to gain understanding and practical experience. Especially in RNA-seq, a growing number of public domain datasets is making it possible to try out bioinformatics in real life without access to a lab or a sequencer. The Pine Biotech team ...
news education rna-seq written 2.9 years ago by Tom Koch110
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Comment: C: Extract Reads From A Bam File That Fall Within A Given Region
... Use "index" from samtools, [described here][1]. samtools index test.bam [1]: http://davetang.org/wiki/tiki-index.php?page=SAMTools#Creating_a_BAM_index_file ...
written 3.0 years ago by Tom Koch110
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Answer: A: Samtools And Region List
... Sorry for the bump (it's for future Google visitors), I used cl.parallel's answer as slight guidance but I wanted to get the same region across a set of reads, so I wrote a script. Uses a BED file as input. for i in $( ls *.bam ); do samtools view $i -H > OUTPUTPREFIX${i%.bam}.sam whil ...
written 3.3 years ago by Tom Koch110
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Comment: C: Extract Sequences From [Gtf File] + [Genome Fasta File], combine matching XLOCs
... Is that Python or something? Sorry, not really a programmer yet.  ...
written 3.3 years ago by Tom Koch110
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Comment: C: Extract Sequences From [Gtf File] + [Genome Fasta File], combine matching XLOCs
... Hi, the Transcriptome technique seems to have worked, but what is the best way to remove the transcript id and replace gene_id with transcript id? I am not good with awk and this seems like a bad job for Excel, so... any help would be appreciated. ...
written 3.3 years ago by Tom Koch110
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Quick command to split BLAST output by Query?
... I used local blastn on a transcriptome of XLOC/TCONS lines from a prior mapping job. The resulting file is over 8GB, and so I attempted to use split on the text file using the -p Query\= pattern filter. It worked, but, when split got to xzz, it stopped, and spit out split: too many files I found ...
blast split written 3.3 years ago by Tom Koch110
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Comment: C: Extract Sequences From [Gtf File] + [Genome Fasta File], combine matching XLOCs
... I was asked to concatenate XLOCs so that the results could be BLASTed, and no, I'm not doing the sequencing without a GTF, there are many genes that are properly identified with non XLOC ids. I will give your suggestion a try. ...
written 3.3 years ago by Tom Koch110
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Comment: C: Extract Sequences From [Gtf File] + [Genome Fasta File], combine matching XLOCs
... XLOC in GTF: http://pastebin.com/WW5aNfZH ...
written 3.3 years ago by Tom Koch110
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Extract Sequences From [Gtf File] + [Genome Fasta File], combine matching XLOCs
... Hi, I found someone, years ago, had a very similar (almost the exact same) question, but it involved using Galaxy, and I would like to use the command line. My goal: Take a sequence of XLOC exons, get their sequences from the genome, and concatenate them. Perhaps blast them afterward, but that can ...
genome rna-seq blast bash written 3.3 years ago by Tom Koch110 • updated 3.3 years ago by geek_y9.6k

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Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: List Of Cloud Genomics Companies

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