User: mb2subi

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mb2subi0
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Posts by mb2subi

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Loss of reads during realignment bam
... It worked perfectly thanks! ...
written 6 months ago by mb2subi0
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Loss of reads during realignment bam
... I everyone, I am trying to realign a bam file from hg37 to hg38. The problem is that I am losing half of the reads while the process. The fastq is paired-end. Here the samtools flagstat for both: Raw bam (hg37) 2457420710 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary ...
wgs gatk samtools bwa fastqvalidator written 6 months ago by mb2subi0
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Comment: C: ASEReadCounter More then one variant context at position
... But theoretically with SelectVariants I should have corrected this "error", right? If not, how I can avoid this positions with more than one variant? ...
written 7 months ago by mb2subi0
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Comment: C: ASEReadCounter More then one variant context at position
... Theoretically the vcf is of SNPs only. I align using bwa -mem but I can try with bowtie2 --local I used allelecounter but the follow advice arose: Traceback (most recent call last): File "/imppc/labs/lplab/share/marc/repos/allelecounter/allelecounter.py", line 177, in main() ...
written 7 months ago by mb2subi0
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Comment: C: ASEReadCounter More then one variant context at position
... chr1 1056601 . A G chr1 1056601 . A ACGTGTGGGTGCGTGTG chr1 105660121 . C T ...
written 7 months ago by mb2subi0 • updated 7 months ago by Pierre Lindenbaum124k
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ASEReadCounter More then one variant context at position
... Hi everyone, I am doing an allelic imbalance of ATAC-seq data using a vcf generated with Strelka2. I used the ASEReadCounter of GATK: java -jar $GenomeAnalysisTK \ -R $reference \ -T ASEReadCounter \ -o $out \ -I $bam \ -sites $vcf But this error arosed: ##### ER ...
selectvariants gatk asereadcounter written 8 months ago by mb2subi0 • updated 8 months ago by Charles Warden7.3k
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Comment: C: java.lang.OutOfMemoryError: Java heap space not solve with -Xmx
... How can split properly the fq.gz for doing the resynchronization? ...
written 9 months ago by mb2subi0
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Comment: C: java.lang.OutOfMemoryError: Java heap space not solve with -Xmx
... Thanks. By the way, isn't possible to do something with the heap space? ...
written 10 months ago by mb2subi0
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Comment: C: java.lang.OutOfMemoryError: Java heap space not solve with -Xmx
... The point is that won't be easy to ask them, for this reason first I'm trying to resolve by myself, if it's not possible the last option will be to ask them. ...
written 10 months ago by mb2subi0
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Comment: C: java.lang.OutOfMemoryError: Java heap space not solve with -Xmx
... The facility sent it out of sync ...
written 10 months ago by mb2subi0

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