User: Ankit

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Ankit130
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Posts by Ankit

<prev • 88 results • page 1 of 9 • next >
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Comment: C: Script to download fasta seqeuences for FGF1 to FGF12
... You can try using bedtools getfasta. 1. First obtain coordinates of the gene (eg. FGF1 and genome version hg19). >chr5 141971743 142077635 FGF1(GRCh37/hg19) (note: tab-separated) 2. Run getfasta using fasta file hg19 version: >bedtools getfasta -fi hg19.fa -bed FGF1.bed -fo FGF1.fa FGF1.f ...
written 22 days ago by Ankit130
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Answer: A: featureCounts log: "WARNING contig is not found in the provided genome file!"
... Did you sort your bam by readname or by coordinates? You can try sorting as per the required input to feature counts. If your contig is not too large. You can upload the bam in igv and manually count the reads and correlate with featurecounts output. If it is too large run bedtools coverage to se ...
written 23 days ago by Ankit130
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Comment: C: Bedtools option suggestion
... Try bedtools closest. https://bedtools.readthedocs.io/en/latest/content/tools/closest.html ...
written 25 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... Yes Devon. You are right. Thank you for suggestion. ...
written 25 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... Thanks genomax for the suggestion. ...
written 26 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... Thanks Devon. I was using awk manually. I also found a function in R resize(), which can do the same. Thanks ...
written 26 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... Yes I used awk already. However I was looking for available tools to do that (to complement the awk). Thanks ...
written 26 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... Ok after searching with different keywords, I found this. [resize][1] library("rtracklayer") userRanges <- import.bed("userFile.bed") library("GenomicRanges") resizeRanges <- resize(userRanges, width = 125) export.bed(resizeRanges, "resizeFile.bed") This is what ...
written 26 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... My input file is BED not fastq. It is a mapped data. reformat.sh Supports sam, fastq, fasta, fasta+qual, scarf, gzip, zip. I do not want to retain or filter reads above or below 125bp. I want to trim all my reads to read length 125bp. For example , if I have 2million reads of read length 125-24 ...
written 26 days ago by Ankit130
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Comment: C: How to bring all reads to the same length? Any tool?
... I do not want to get reads that are below or above 125bp. I have reads longer than 125 bp (some n numbers). The length of these reads are 125-240. I want to make all of them 125bp. Is it possible? I used a awk command to do that. But I want to do that with a tool. Of course the strand informati ...
written 26 days ago by Ankit130

Latest awards to Ankit

Supporter 25 days ago, voted at least 25 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
Popular Question 10 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq

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