User: sruthi

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sruthi0
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Posts by sruthi

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Microsatellite Instability, Whole exome sequencing
... Hey Nicolas, I tried using this command and it says "please provide a valid format normal bam file!" What should I do now? TIA ...
written 14 hours ago by sruthi0
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Comment: C: Microsatellite Instability: msiSENSOR
... The error is rectified. ...
written 14 hours ago by sruthi0
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Comment: C: Microsatellite Instability: msiSENSOR
... Command: msisensor -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix ...
written 1 day ago by sruthi0
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Microsatellite Instability: msiSENSOR
... Hi, I'm new to Microsatellite instability and trying to work on msiSENSOR tool. I tried uploading a bam file in msisensor using the command: msisensor -d microsatellites.list -t tumor.bam -o output.tumor.prefix And it says: failed to open homopolymers and microsatellites file I checked the path an ...
next-gen sequencing written 1 day ago by sruthi0
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Pool of Normals- PureCN
... Hi, I read that, 10 or more of normal samples would be sufficient to build PureCN -PoN and that the exome must have been enriched using the same capture kit as for tumor exome. What if, there are less/no exomes enriched with the same capture kit available? Can samples enriched using different captur ...
next-gen sequencing written 7 days ago by sruthi0 • updated 6 days ago by markus.riester320
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Comment: A: PureCN: Estimating tumor purity and ploidy
... Hey, I would also like to know whether IDT xgen provides hg38.bed file. While looking for .bed files on their website, I could find only the one for hg19 and not hg38. Could you please give me a clarity on this? TIA Sruthi ...
written 7 days ago by sruthi0
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Comment: C: PureCN: Estimating tumor purity and ploidy
... No. I will align the BAM file again and then run the tool. Thanks Markus ...
written 7 days ago by sruthi0
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Comment: C: PureCN: Tool for estimation of tumor purity and ploidy
... Thanks Markus. I will open an GitHub issue. ...
written 7 days ago by sruthi0
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PureCN: Estimating tumor purity and ploidy
... Hi, I tried calculating GC normalized coverage by giving .bam file and intervals.txt file as input and the following error showed up. I tried viewing the BAM file for the error, but file size being big, it ain't happening. What should I do to troubleshoot the error? Error in .io_bam(.scan_bamfile, ...
next-gen sequencing written 14 days ago by sruthi0
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Comment: C: PureCN: Tool for estimation of tumor purity and ploidy
... Thanks Markus. I uploaded a BED file with capture baits, but the same error pops up. Is there something that I must look in the FASTA file? Also, which build is supported by the tool? hg19 or hg38. ...
written 15 days ago by sruthi0

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