User: shubhra.bhattacharya

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Posts by shubhra.bhattacharya

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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 24 days 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 9 weeks ago by shubhra.bhattacharya40 • updated 4 days 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 9 weeks ago by shubhra.bhattacharya40 • updated 9 weeks ago by svlachavas430
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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 3 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 3 months ago by shubhra.bhattacharya40
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Difference in TASSEL4 and TASSEL5
... Hi everyone I am using both TASSEL4 and TASSEL5 with the same data set. I have noticed that the fastq file created by them(using FastqToTagCountPlugin and TagExportToFastqPlugin respectively) has a astounding difference in terms of number of reads. I am curious to know what might be the differenc ...
tassel gbs written 3 months ago by shubhra.bhattacharya40
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Genotyping by Sequencing: TASSEL and UNEAK
... Hi all, I have a few queries regarding GBS using TASSEL UNEAK Pipeline. This post might be a bit lengthy. > I have 100 sample data of withania somnifera. This does not have a > reference genome. It was decided to use UNEAK pipeline for GBS. UNEAK > does not require a reference genome. Usi ...
gbs written 4 months ago by shubhra.bhattacharya40 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: FreeBayes Variant Diversity capture
... Yes I am sure that the same reference sequence was used in alignment and variant calling. ...
written 5 months ago by shubhra.bhattacharya40
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FreeBayes Variant Diversity capture
... I have used FreeBayes for variant calling after facing some issues with GATK. The bam file which FreeBayes requires as a mandate is 53 Gb in size. The command used is: > /data/programs/freebayes/bin/freebayes -f Reference.fasta Realign-AB.bam > Bayes-AB.vcf & When i check for the differ ...
snp written 5 months ago by shubhra.bhattacharya40
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Answer: A: how to haplotyping from vcf file?how to analysis ld block?
... Try Genotypevcf in GATK. ...
written 5 months ago by shubhra.bhattacharya40

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