User: Susmita Mandal

Reputation:
60
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Trusted
Location:
Bangalore
Last seen:
3 weeks, 6 days ago
Joined:
1 year, 6 months ago
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s*****************@gmail.com

Posts by Susmita Mandal

<prev • 72 results • page 1 of 8 • next >
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Does Nextera Transposase adapter sequence affects GATK HaplotypeCaller pipeline?
... Hi, I trimmed my paired end fastq data using Trimmomatic using TruSeq-PE adapters, but actually they contain Nextera transposase adapter sequences. I have already aligned and did variant calling using GATK "HaplotypeCaller". Would the adapter contamination will affect the variant calling? Please h ...
gatk ngs snp rna-seq illumina written 6 weeks ago by Susmita Mandal60
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Comment: C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
... I am very sure. It's not publicly available data. ...
written 8 weeks ago by Susmita Mandal60
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Comment: C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
... So there is no way to avoid that, in an unstranded RNA-Seq? :( ...
written 8 weeks ago by Susmita Mandal60
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Comment: C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
... Well I'm doing by creating personalized genomes (mouse strains). By overlapping I mean, lets take Xist and Tsix, antisense to each other, but most of the reads are coming from the same allele in these genes and other genes too. Could it be a case of allelle mapping bias? ...
written 8 weeks ago by Susmita Mandal60
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Comment: C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
... The thing is I have tried this command and I'm getting overlapped reads between the two strands and it should not happen. I'm doing allele specific variant calling. I should say the rna-seq is not strand-specific, would that be an issue? ...
written 8 weeks ago by Susmita Mandal60
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Comment: C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
... I did looked at it and many other web pages and I'm more confused now ...
written 8 weeks ago by Susmita Mandal60
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Split BAM file from paired end read into forward and reverse strand w.r.t reference genome
... Hello, I have a paired end data and I have an alignment file (SAM/BAM). I want to split it into forward and reverse strand w.r.t reference genome. Looking at the SAM file, I am getting reads having 83,163,99 and 147 flags. So which flags I should consider for forward and reverse? Please help me out ...
variant calling ngs samtools rna-seq snp written 8 weeks ago by Susmita Mandal60 • updated 8 weeks ago by ATpoint32k
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Comment: C: SAM flags meaning
... I am understanding the SAM flags to some extent. But I have a paired end data and I have mapped it to a reference genome and I would like to split that BAM file into plus and minus strands w.r.t. reference genome. So i don't understand how to go about it. Please help me. ...
written 9 weeks ago by Susmita Mandal60
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Tools and/or methods to detect allelic mapping bias.
... Hello, I would like to know what are various kinds of tools and/or methods that can detect allelic mapping bias in a RNA-Seq data. Any papers/tools/methods/R packages links is appreciated. Although if someone has personally used the said methodology would be better. Best, Susmita ...
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Comment: C: Making pattern of GT:AD:DP:PL column values to be replaced by o and 1.
... Did you try using awk? ...
written 10 weeks ago by Susmita Mandal60

Latest awards to Susmita Mandal

Popular Question 6 weeks ago, created a question with more than 1,000 views. For coverage of a SNP site?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For How to include genes having negative fold change in the log2 FC plot?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to include genes having negative fold change in the log2 FC plot?
Popular Question 6 months ago, created a question with more than 1,000 views. For LiftOver a VCF file
Popular Question 7 months ago, created a question with more than 1,000 views. For LiftOver a VCF file
Popular Question 7 months ago, created a question with more than 1,000 views. For Allele Specific Expression Analysis

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