User: a01039012387

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a0103901238710
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Last seen:
10 months ago
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1 year, 9 months ago
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Posts by a01039012387

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Answer: C: GDC portal data download
... I put the -s parameter since the GDC url was changed and it worked. And as your comment, I reobtain the ID from a file manifest and It's working! I seem to have made a mistake while getting the ID. I do not know why the error message says the token is a problem, though. Thank you so much for your h ...
written 10 months ago by a0103901238710
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Comment: C: GDC portal data download
... I have approved access and download a new token just before running the command but it still not working. ...
written 10 months ago by a0103901238710
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GDC portal data download
... Hello. I'm trying to download some TCGA WXS data from GDC portal using gdc-client, but it's not working. It just shows the error message like below even though I use new token. ERROR: Unable to download 9bb44eab-cf7f-4335-ba58-1fe8e815f4a8: 403 Client Error: FORBIDDEN: { "message": "Your ...
tcga gdc download gdcportal written 10 months ago by a0103901238710
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Comment: C: Varscan fpfilter error
... Oh, thanks for the reply. Here is my entire commend for Varscan, and I already using varscan2.4.3. > export GENOME=/home/bin/genome.fa > samtools mpileup -f $GENOME -q 1 -B $path_new_bam_normal $path_new_bam_tumor > $path_mpileup > java -jar VarScan.v2.4.3.source.jar somati ...
written 10 months ago by a0103901238710
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Varscan fpfilter error
... Hello. I'm new to Varscan. I want to call the SNPs from the bam file using varscan in the order of somatic - processSomatic-fpfilter but I got an error message in the fpfilter process. Here is my command. perl fpfilter.pl --var-file [snp.Somatic.hc] --readcount-file [readcount] --output-file [ ...
varscan snp fpfilter bam-readcount somatic written 10 months ago by a0103901238710 • updated 10 months ago by RamRS21k
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converting varscan2 output to sequenza
... Hi. I'm trying to run a sequenza with the output of varscan2 I used VarScan version of 2.4.3 and put into sequenza but I got an error message "Error in data.frame(chromosome = as.character(varscan.somatic$chrom), : arguments imply differing number of rows: 0, 1" ---------- This is my output ...
exome wes mutation snp written 21 months ago by a0103901238710 • updated 15 months ago by nilesh.gardi26880
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"sequenza" - chromosomes are removed when I run 'sequenza.extract'.
... Hi. I'm trying to run a "sequenza", but something is wrong. Before I made a pileup file, the bam file has chromosome 1 - 22 and X, Y but when I run a sequenza.extract, there is only chr1. > test <- sequenza.extract("out_PAAD_small.seqz.gz") Processing chr1: 42 variant calls; 2970 heterozygou ...
wxs sequenza written 22 months ago by a0103901238710
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I need allele copy number information for running PyClone
... Hello. I'm new with pyclone and I'm trying to run a pyclone with WES data from TCGA. I need some information of allele specific copy number to make a input file for pyclone, but i don't know which tools I can use for it. I downloaded somatic mutation output of mutect file from TCGA and it has t_de ...
wes whole-exome allele copy number written 22 months ago by a0103901238710 • updated 15 months ago by nilesh.gardi26880

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Scholar 10 months ago, created an answer that has been accepted. For C: GDC portal data download

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