User: genya35

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genya350
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Posts by genya35

<prev • 80 results • page 1 of 8 • next >
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Comment: C: tools for Microsatellite Instability Identification
... yes, but it's not working well with IonTorrent single-end targeted data. Thanks ...
written 20 days ago by genya350
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macrosatellite instability regions important in cancers
... Hello, Could someone please suggest where I can obtain a list of hg19 microsatellite instability regions that are important in different tumor types. Thank you. ...
sequence written 4 weeks ago by genya350 • updated 4 weeks ago by Kevin Blighe28k
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tools for Microsatellite Instability Identification
... Hello, Could someone please suggest free tools that can be used on single-end reads amplicon based ngs data for Microsatellite Instability Identification. Thank you ...
next-gen written 5 weeks ago by genya350
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Comment: C: how to run bioinformatics tools via docker
... I'm trying to run fusioncatcher in somatic mode but it's not working: `docker run --rm -v /home/genya7/mst/rna_seq/:/data vimalkvn/fusioncatcher-nodb /opt/fusioncatcher/v1.00/bin/fusioncatcher-batch.py -i /data/tumor/ -n /data/normal/ -o /data/output_90530/`; It's working in this mode: ...
written 6 weeks ago by genya350
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Comment: C: finding mutations in rna-seq transcriptome
... @jared.andrews07 is VarScan2 same as VarScan version 2? Should I Split'N'Trim and reassign mapping qualities with SplitNCigarReads before running samtools to generate mpileup, and finally run VarScan in somatic mode? Thanks ...
written 8 weeks ago by genya350
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Comment: C: finding mutations in rna-seq transcriptome
... I forgot to mention, that I have both tumor and normal fastqs and looking for somatic mutations. Is GATK best practices still appropriate? Thanks ...
written 9 weeks ago by genya350
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Comment: C: Alternative tools to SplitNCigarReads
... It's not available on Galaxy. ...
written 9 weeks ago by genya350
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Alternative tools to SplitNCigarReads
... Hello, Could someone please suggest an alternative tool to GATK's SplitNCigarReads, preferably available on Galaxy? Thanks, Lena ...
rna-seq written 9 weeks ago by genya350
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Comment: C: write Pindel error to text file
... Pindel works well with KIT indels but misses some EGFR indels. ...
written 3 months ago by genya350
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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 3 months ago by genya350

Latest awards to genya35

Popular Question 28 days ago, created a question with more than 1,000 views. For convert fasta dna files to protein
Popular Question 28 days ago, created a question with more than 1,000 views. For hisat2 command line fastq to bam
Popular Question 13 months ago, created a question with more than 1,000 views. For convert fasta dna files to protein

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