User: kirannbishwa01

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Posts by kirannbishwa01

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Comment: C: detecting allele specific expression of a gene at a specific locus without havin
... That sounds good that it is working. :) ...
written 6 days ago by kirannbishwa01530
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Comment: C: detecting allele specific expression of a gene at a specific locus without havin
... yeah, I have come across MBASED, but I think its for comparing ASE between two replicates of same sample. It may be otherwise, but I would look into the assumptions made by the tool/author in detail, before relying on ASE report. ...
written 7 days ago by kirannbishwa01530
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Answer: A: detecting allele specific expression of a gene at a specific locus without havin
... Check this software: https://www.nature.com/articles/srep21134 i.e GeneiASE, but I have not used it personally. The big deal in ASE analyses is that we are making assumptions that both the alleles have equal likelyhood of mapping, but the actual scenario is different (there is a mapping bias). So, ...
written 12 days ago by kirannbishwa01530
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Comment: C: How to plot coverage and depth statistics of a bam file
... I read all the answers/comments on this one. But, I have different opinion regarding this problem. `No matter how much deep sequencing you do (even in whole genome) there is a good probability that there will be good amount of genomic regions with 0 depth.` The reason is with short reads it is diffi ...
written 7 weeks ago by kirannbishwa01530
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Comment: C: How to plot coverage and depth statistics of a bam file
... Hi @bioinfo8, just gettting back to this problem a little late. I think you can totally use the code I shared in my answer - using `Samtools depth`. I think I understand coverage of multiple bam files - i think you have 23 samples (rite??) and you want to plot the coverage for same chromosome from d ...
written 7 weeks ago by kirannbishwa01530
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Comment: C: How to force merge a VCF files, for different samples?
... Hi @WouterDeCoster. How are you doing? Yeah, I used a a toold called phase to phase my variants, which unfortunately in the recent version had a bug and didn't add `PG` tag in the header. I have to merge different vcf files that came out of this tool, but I am getting error on every tool that does ...
written 3 months ago by kirannbishwa01530
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How to force merge a VCF files, for different samples?
... I obtained vcf files from a tool I used. I want to merge them but it was missing some TAG info, which I fixed. Now, I am having somekind of ERROR probably emerging again from HEADER. Is there a way to force merge vcf files, if not fix the vcf files. I don't really care much about HEADER at this tim ...
vcf genome merge snp written 3 months ago by kirannbishwa01530 • updated 3 months ago by Istvan Albert ♦♦ 73k
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Comment: C: RNA-seq: Explain STAR quantMode geneCounts values
... Good explanation. Really helped with the clearing out the doubts. Thanks, ...
written 3 months ago by kirannbishwa01530
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How to count the number of unique alignment in PE reads? How to account for unmapped mate?
... I am trying to find the number of reads that align uniquely, to two, to three and multilocations in a bam file. This bam was create using PE reads and below is two lines from the SAM file: HWI-D00123R2:155:C4AM3ACXX:2:1103:4696:31199 403 AL2G13910.t1 5619 60 100M = 5586 -133 GAGATAGTGGAATCATCC ...
genome count bam alignment written 3 months ago by kirannbishwa01530
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Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
... **One of the situation when bam to fastq conversion might be required:** Say, I have a problem where I want to take the reads that are aligned to **chromosome 2** of one species. And, I want to see how much (fraction) of these same reads align to **chr 2** of another species or population and with ...
fastq bam samtools tutorial alignment sequence written 3 months ago by kirannbishwa01530

Latest awards to kirannbishwa01

Popular Question 1 day ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 6 days ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Popular Question 3 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Scholar 3 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Popular Question 4 months ago, created a question with more than 1,000 views. For Changing @RG header information in *.bam files using picard
Scholar 5 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: How to plot coverage and depth statistics of a bam file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to plot coverage and depth statistics of a bam file
Scholar 7 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to plot coverage and depth statistics of a bam file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to plot coverage and depth statistics of a bam file
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Scholar 12 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
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