User: kashifalikhan007

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Cologne
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1 day, 22 hours ago
Joined:
3 years, 8 months ago
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Posts by kashifalikhan007

<prev • 15 results • page 1 of 2 • next >
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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 6 days 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 3 months ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... remove this: -num_alignments 5 ...
written 5 months ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... what command you have used for blastall? ...
written 5 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 5 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 5 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 5 months ago by kashifalikhan00740
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Answer: A: Combining two columns in a tab-delimited file where there is a zero in one
... If both column are in different files, first convert both your file in txt. Then: paste blastx.txt blastp.txt | awk '{if($1=="0")print$2"\t"$2; else print}' > ur_output.txt If in same file: awk '{if($1=="0")print$2"\t"$2; else print}' input.txt > ur_output.txt ...
written 5 months ago by kashifalikhan00740
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Answer: A: MCScanX result problem
... Can you check your gff and blast.output file? The chr name should be same in both. And the blast.output should contain weed-weed, weed-maize, maize-weed and maize-maize while your gff should have weed the maize. ...
written 5 months ago by kashifalikhan00740
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Answer: A: Question: Converting Blast Results/Output to FASTA format
... grep "^Acan" ur_blast.output | awk '{print">query: "$1"\tHit: "$2"\tscore: "$4":"$5":"$6"\n"$3}' > ur_result.output ...
written 5 months ago by kashifalikhan00740

Latest awards to kashifalikhan007

Scholar 5 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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