User: Susmita Mandal

Reputation:
40
Status:
New User
Location:
Bangalore
Last seen:
4 weeks ago
Joined:
9 months ago
Email:
s*****************@gmail.com

Posts by Susmita Mandal

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Moving average plot of gene expression ratio along the chromosome length
... Will it work if I want to check the ploidy of X chromsome in my samples. It's single cell RNA -Seq. ...
written 5 weeks ago by Susmita Mandal40
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Comment: C: Moving average plot of gene expression ratio along the chromosome length
... Can you explain this > averaging signal across samples and then making bigWigs of the ratio between each sample ...
written 5 weeks ago by Susmita Mandal40
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Moving average plot of gene expression ratio along the chromosome length
... Hello, I would like to see any chromosomal abberations in my samples and for that I want to plot moving average plots using expression values. Does anyone has any idea how to make one and what all tools I can use? Also how to find the positions of all the genes of a chromosome in humans? Any help w ...
gene R bioconductor next-gen rna-seq written 5 weeks ago by Susmita Mandal40
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Comment: C: Convert RefseqID to EntrezID
... Sorry I don't think it has Oryzias latipes ...
written 5 weeks ago by Susmita Mandal40
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Comment: A: Convert RefseqID to EntrezID
... https://www.biotools.fr/ Try this ...
written 5 weeks ago by Susmita Mandal40
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Comment: C: Getting only Indels and no SNPs after variant calling variant calling using Hapl
... I got SNPs after removing --outFilterMismatchNmax 0 in my mapping step! ...
written 5 weeks ago by Susmita Mandal40
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Comment: C: Allele specific expression analysis using human cell line
... Hi, You can use SNPsplit if you have the parental SNP data. Or you can make a vcf file containing positions that are heterozygous, i.e; one from paternal and another from maternal, and then using that vcf file, do variant calling with HaplotypeCaller of GATK. You can use VarScan2 also for that matte ...
written 5 weeks ago by Susmita Mandal40
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Comment: C: Getting only Indels and no SNPs after variant calling variant calling using Hapl
... I have gotten SNVs using this option previously. ...
written 5 weeks ago by Susmita Mandal40
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Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller
... Hello everyone, I am running HaplotypeCaller by GATK for variant calling and I'm getting only indels and no SNPs. I happen to know that the sample contains SNPs as I'm reproducing the data from another paper. Following is the code that I'm following. Let me know where I'm making a mistake or there ...
variant calling gatk bam rna-seq snp written 5 weeks ago by Susmita Mandal40
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Is it advisable to do allele specific expression analysis on single cell RNA-Seq data?
... Hello everyone, I want to do allele expression analysis on single cell RNA-Seq data. I read in a paper that it's always better to do ASE on a cell population rather than on single cells, cause in the latter there is always chance of allelic imbalance. So is it true or it can be done with some trick ...
single-cell ngs ase rna-seq snp written 3 months ago by Susmita Mandal40 • updated 11 weeks ago by Biostar ♦♦ 20

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