User: Ankit

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Ankit60
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Posts by Ankit

<prev • 32 results • page 1 of 4 • next >
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Comment: A: Seqmonk: Bedgraph as input ? (EPIC methylation array data)
... Any suggestions???? Thanks ...
written 7 weeks ago by Ankit60
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Seqmonk: Bedgraph as input ? (EPIC methylation array data)
... Hi everyone, Is it possible to give Bedgraph of methylation data as input to Seqmonk? I do not have .cov or .bam. because the data is from EPIC methylation array. I only have Bedgraph. I uploaded it as text file but it is not giving me strand separated view and rather like a line as in bed file ...
seqmonk bedgraph probe design methylation written 7 weeks ago by Ankit60 • updated 7 days ago by Charles Warden6.1k
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Comment: C: bedtools multicov - tab-delimited bam files?
... What is the command of your bedtools multicov? Did you sort your bam and indexed? ...
written 11 weeks ago by Ankit60
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Comment: C: How to extract read-pairs that aligned multiple times?
... Hi. You can filter out multiple aligned reads using XS:i tags in SAM file. ...
written 12 weeks ago by Ankit60
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Comment: C: Allele Specific Expression Analysis
... Hi, After alignment you can use bedtools to intersect your bam or bed on SNP coordinates and extract only those reads which overlap SNPs. ...
written 12 weeks ago by Ankit60
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Comment: C: No mismatch allowed setting in Bowtie2 (-N 0 does not help)
... Hi Santosh, Thank you for the suggestion. So I ran QuasR pieline for Allele Specfic analysis. The output is not so useful, because it generated a combined bam file for alignment on two different genome.So in the end there is no way I can discriminate between the two alleles and only I can count to ...
written 12 weeks ago by Ankit60
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Comment: C: if I have a SNP on the cDNA level, how can I find the corresponding mutation on
... Hi. Just simply annotate the VCF file. Use ANNOVAR or Snpeff. You can even upload the VCF to wANNOVAR, which will give you the annotated files. The anotated file will have both cDNA change and protein change. ...
written 12 weeks ago by Ankit60
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Comment: C: No mismatch allowed setting in Bowtie2 (-N 0 does not help)
... Hi Santosh, Thanks for the reply > You should also check for any adapter contamination > you should double check that the sequencing quality is good (fastqc) So I checked the quality there is no adapter contamination which I removed prior to starting analysis. > An alternative way to y ...
written 3 months ago by Ankit60
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Comment: C: No mismatch allowed setting in Bowtie2 (-N 0 does not help)
... Hi Santosh, Thanks for the reply. > like give high penalty to Gap open and extend (--rdg and --rfg) or change --score_min (lets make it positive), So If there is a choice between setting --score-min or --rdg , --rfg, which one is good to choose. As I have discussed before, I have set --score ...
written 3 months ago by Ankit60
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Comment: C: No mismatch allowed setting in Bowtie2 (-N 0 does not help)
... Hi Santosh, Thanks for suggestion, So I ran the pipeline. Here is the command: bowtie2 -p 10 --mp 10000,10000 --ignore-quals -x /home/ref_av/mm9_bowtie2/mm9 -U my_trimmed.fastq -S my.mpsant.sam The problem is still there: The reads containing mismatch are still present in output sam file: ...
written 3 months ago by Ankit60

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