User: shubhra.bhattacharya

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s*******************@genotypic.co.in

Posts by shubhra.bhattacharya

<prev • 25 results • page 1 of 3 • next >
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Comment: C: mice whole Exome sequencing Analysis
... You can look into mutect: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php ...
written 4 weeks ago by shubhra.bhattacharya40
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(Closed) PCA for SNPs
... Hi! Can someone tell me is there a way by which I can perform PCA on variants and plot them as well? I tried to read the PLINK pca page but I cannot make my way through it. My input will be .vcf file. Thanks!! ...
snps pca written 6 weeks ago by shubhra.bhattacharya40
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Comment: C: Explain the definition of DELLY output
... https://groups.google.com/forum/#!msg/delly-users/6Mq2juBraRY/Pj4NVGdvHAAJ ...
written 7 weeks ago by shubhra.bhattacharya40
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Comment: C: Explain the definition of DELLY output
... I have the same issue as indicated in the link below. Specially how co-ordinates are mapped during translocation events. https://www.biostars.org/p/328924/ ...
written 8 weeks ago by shubhra.bhattacharya40
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Comment: C: GT (genotype information) in haploid organism has a value of 2 .
... Yes I specified the ploidy as haploid. ...
written 8 weeks ago by shubhra.bhattacharya40
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Answer: A: number of functions is more than namber of variants in snpEff's output
... Hello guys! was this problem resolved I am getting the same issue now. ...
written 4 months ago by shubhra.bhattacharya40
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GT (genotype information) in haploid organism has a value of 2 .
... Dear all, Although this question may seem a bit trivial but can someone please explain what the GT field (0,1,2) imply in case of haploid organism. I called SNP's using Haplotype caller. A typical entry is indicated below: NW_001091929.1 14514 . T A 56.12 . AC=0;AF ...
genotype snp written 5 months ago by shubhra.bhattacharya40 • updated 3 months ago by Biostar ♦♦ 20
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Data set to perform DGE
... Hello everyone, I want to get a hands-on with learning transcriptomics. Can someone please guide me as to where I can find data set to learn transcriptomics. I am a beginner to the field and do not have access to any data set to utilise what I read in papers. ...
trancriptomics dge written 5 months ago by shubhra.bhattacharya40 • updated 5 months ago by svlachavas480
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Comment: C: [ti_index_core] the chromosome blocks not continuous at line xxxx, is the file s
... 5891581 chrMT 16129 G A 5891582 chrMT 16129 G A 5891583 chrMT 16179 CAA C 5891584 chr1 3088286013 AAA CCC 5891585 chrMT 16182 A C 5891586 chrMT 16183 A C 5891587 chrMT 16186 C T 5891588 chrMT 16188 C T 5891589 chrMT 16189 T C This is the output of the command. The chr1 is just dropping by in b/w t ...
written 6 months ago by shubhra.bhattacharya40
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[ti_index_core] the chromosome blocks not continuous at line xxxx, is the file sorted? [pos 1]
... While using tabix I encounter the following error. > [ti_index_core] the chromosome blocks not continuous at line 5891584, > is the file sorted? [pos 1] Command: /data/ngs/programs/tabix-0.2.6/tabix -p vcf SRR12954_1.fastq.gz_20180228112323.GRCH38.vcf.gz I have zipped the vcf file using bg ...
vcf variant index written 6 months ago by shubhra.bhattacharya40

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