User: kashifalikhan007

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Cologne
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3 years, 12 months ago
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Posts by kashifalikhan007

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Finding Minisatellite Repeat Motives In Dna
... Hi @Haibao, Can you tell me where to find the description for bed output from trfBig. I am completely confused with the bed output because there is no header on the file. ...
written 27 days ago by kashifalikhan00740
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Comment: C: How to extract bigWig signal for a given bed file?
... Ohh... thanks I have used it, but completely forgotten. ...
written 3 months ago by kashifalikhan00740
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Comment: C: How to extract bigWig signal for a given bed file?
... I think it will be helpful if one is plotting the nucleosome signal around TSS or TTS. As some genes has reverse orientation (negative strands in gff file), there data needs to be reversed accordingly before plotting. Correct me if I am wrong. ...
written 3 months ago by kashifalikhan00740
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Comment: C: How to extract bigWig signal for a given bed file?
... cool library... does this also takes care about negative and positive strands from bed file? ...
written 4 months ago by kashifalikhan00740
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Answer: A: Binning Exon And Plotting Read Densities (Bed Regions) With In And Around Binned
... solution is here https://deeptools.readthedocs.io/en/latest/content/list_of_tools.html ...
written 7 months ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... remove this: -num_alignments 5 ...
written 8 months ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... what command you have used for blastall? ...
written 9 months ago by kashifalikhan00740
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Comment: C: Compare mus musculus and mus spretus genome structure annotation
... You can use any annotation comparison tools. I found [MCScanX][1]. more useful. Along with the homologs (both paralogs and orthologs) it alos determines duplicates, tandem repeats, collinearity, gene family tree and few more. It can also calculate the ka ks value using which you can track time of ...
written 9 months ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... As you can see, you have ".t1" is present with gene name in blast output file, but not in gff file. Either remove it from blast output or add to gff file. ...
written 9 months ago by kashifalikhan00740
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Answer: A: chrom.sizes computed locally
... Try samtools samtools faidx genome.fa cut -f1,2 genome.fa.fai > genome.size ...
written 9 months ago by kashifalikhan00740

Latest awards to kashifalikhan007

Scholar 9 months ago, created an answer that has been accepted. For A: Combining two columns in a tab-delimited file where there is a zero in one

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