User: yelekley7

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yelekley70
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Posts by yelekley7

<prev • 72 results • page 1 of 8 • next >
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Comment: C: write Pindel error to text file
... Pindel works well with KIT indels but misses some EGFR indels. ...
written 12 days ago by yelekley70
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Comment: C: write Pindel error to text file
... sorry, i mean single end and not pair reads. The amplicon size is 125, but error message sometimes goes up to 350. Doesn't make sense. ...
written 12 days ago by yelekley70
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Comment: C: write Pindel error to text file
... Sometimes Pindel overestimates the "insert size" which i assume is the read length for single-pair reads. Do you know? Do you know of any other good indel callers for Ion Torrent single-pair reads somatic(no matching normals)? Thanks ...
written 12 days ago by yelekley70
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write Pindel error to text file
... Hello, I'm running Pindel on small Ion Torrent (single-end reads) bam files. When the insert size specified in the config file is less than detected by the software, Pindel crashes with an error message. Could someone please suggest how to write that error message to a text file? Here is the comma ...
software error written 12 days ago by yelekley70 • updated 12 days ago by Kevin Blighe21k
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Comment: C: finding mutations in rna-seq transcriptome
... Is it possible to use rna-star on usegalaxy.org to do the alignment. I don't see two-pass mode option? It's not clear on the website. ...
written 13 days ago by yelekley70
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Comment: C: finding mutations in rna-seq transcriptome
... What do I use to convert fast-q RNA-seq to bam format? ...
written 13 days ago by yelekley70
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finding mutations in rna-seq transcriptome
... Hello, Please suggest bioinformatics tools to identify indel and point mutations in RNA-seq transcriptome. Thanks ...
rna-seq written 13 days ago by yelekley70 • updated 13 days ago by grant.hovhannisyan880
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how to use bgzip with tabix docker image
... Please suggest how to run `bgzip` via docker image. I've secessfully pulled: https://hub.docker.com/r/mgibio/tabix/builds/ but can't figure out how to run bgzip command. Thanks [1]: http:// ...
software error written 19 days ago by yelekley70 • updated 18 days ago by Gungor Budak190
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Comment: C: docker container for Pindel
... Thanks, your suggestion worked. Could you please suggest how to run `pindel` and `pindel2vcf` via docker? I've tried this: my $cmd1 = `docker run -v /home/yey/mdl3:/data --rm mgibio/pindel:v0.2.5b8 /opt/pindel-0.2.5b8/pindel \ -f /data/reference/chr4.fa \ -i /data/pindel/bam_file ...
written 20 days ago by yelekley70
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docker container for Pindel
... Hello, Could a kind a person please create a docker container for Pindel and post it on Docker Hub. The dockerfile is found here: https://hub.docker.com/r/mgibio/pindel/~/dockerfile/ I can't find an active container and a firewall on my machine is preventing the creation of my own. Thank you ...
software error written 21 days ago by yelekley70

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Popular Question 10 months ago, created a question with more than 1,000 views. For convert fasta dna files to protein

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