User: chahat_u

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chahat_u50
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Posts by chahat_u

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Extract R1 and R2 bam files from merged bam file
... Hi, I tried the command you mentioned and it resulted in the R1 and R2 bam files. But, when I try to do HiC analysis using them, a code in the pipeline that is supposed to merge the 2 bam files gives the error - *## Merging forward and reverse tags ... Forward and reverse reads not paired. Check ...
written 5 weeks ago by chahat_u50
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Comment: C: Extract R1 and R2 bam files from merged bam file
... Thanks a lot for this!! ...
written 5 weeks ago by chahat_u50
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Extract R1 and R2 bam files from merged bam file
... Hi, I started with R1 and R2 fastq files, and using a pipeline ([https://github.com/ArimaGenomics/mapping_pipeline/blob/master/Arima_Mapping_UserGuide.pdf][1]), I combined them to give a merged bam file (it also does other things like filtering for mapping quality, adding read groups and remove PCR ...
samtools rna-seq written 5 weeks ago by chahat_u50 • updated 5 weeks ago by h.mon18k
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Comment: C: Why does this samtools command work?
... Thanks for that explanation, I did not know that before! ...
written 5 weeks ago by chahat_u50
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Comment: C: Why does this samtools command work?
... Got it, so basically the perl script is doing both - merging the 2 bam files, and simultaneously filtering based on map quality. So, if I had to get rid of the merging of the bam files, and still filter the 2 (R1 and R2) bam files, then I can bypass this perl script altogether and do the filtering u ...
written 5 weeks ago by chahat_u50
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Why does this samtools command work?
... Hi, I am trying to map fastq files to bam format, and I am using the pipline mentioned here - https://github.com/ArimaGenomics/mapping_pipeline/blob/master/Arima_Mapping_UserGuide.pdf. One of the commands in the pipeline is - perl $COMBINER $FILT_DIR/$SRA\_1.bam $FILT_DIR/$SRA\_2.bam $SAMTO ...
samtools rna-seq written 5 weeks ago by chahat_u50 • updated 5 weeks ago by h.mon18k
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Answer: A: Insillico dual restriction enzyme reference genome digestion.
... Another good option is a utility called digest_genome(.py) that comes with HicPro. It can digest the reference genome by the provided restriction enzymes(s) and generate a BED file with the list of restriction fragments after digestion. You can specify multiple restriction enzymes too. [here is the ...
written 9 weeks ago by chahat_u50
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Can we look at interactions between host genome and pathogen genome from Hi-C data?
... I have Hi-C data from human cells that were infected with a virus. It's possible that the virus genome interacts with the host (human) genome. Is it possible to find out these interactions from this Hi-C data? (maybe by somehow finding reads that, say, did not match to the human genome, or those th ...
genome human genome interactions genomics written 11 weeks ago by chahat_u50
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Comment: C: Finding restriction sites when the gene is on the negative strand
... Thanks Anima, this was quite helpful. I will let you know if I have any further questions! ...
written 12 weeks ago by chahat_u50
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Comment: C: Finding restriction sites when the gene is on the negative strand
... Thanks @Wouter for the reply. What I am confused is if the restriction sites on the positive strand would map to the same locations on the -ve strand too. Believe me, I have drawn quite a few diagrams since yesterday :) ...
written 3 months ago by chahat_u50

Latest awards to chahat_u

Student 9 months ago, asked a question with at least 3 up-votes. For Low mapped percentage. How to know if data is junk?
Supporter 9 months ago, voted at least 25 times.

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