User: shubhra.bhattacharya
shubhra.bhattacharya • 40
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- 2 weeks, 3 days ago
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- 5 months, 3 weeks ago
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- s*******************@genotypic.co.in
Posts by shubhra.bhattacharya
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... Hello guys!
was this problem resolved I am getting the same issue now. ...
written 24 days ago by
shubhra.bhattacharya • 40
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... 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 ...
written 9 weeks ago by
shubhra.bhattacharya • 40
• updated
4 days ago by
Biostar ♦♦ 20
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... 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. ...
written 9 weeks ago by
shubhra.bhattacharya • 40
• updated
9 weeks ago by
svlachavas • 430
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... 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.bhattacharya • 40
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... 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 ...
written 3 months ago by
shubhra.bhattacharya • 40
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... 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 ...
written 3 months ago by
shubhra.bhattacharya • 40
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... 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 ...
written 4 months ago by
shubhra.bhattacharya • 40
• updated
3 months ago by
Biostar ♦♦ 20
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... Yes I am sure that the same reference sequence was used in alignment and variant calling.
...
written 5 months ago by
shubhra.bhattacharya • 40
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... 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 ...
written 5 months ago by
shubhra.bhattacharya • 40
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... Try Genotypevcf in GATK. ...
written 5 months ago by
shubhra.bhattacharya • 40
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