User: kashifalikhan007

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Cologne
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Posts by kashifalikhan007

<prev • 14 results • page 1 of 2 • next >
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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 16 days ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... remove this: -num_alignments 5 ...
written 8 weeks ago by kashifalikhan00740
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Comment: C: MCScanX result problem
... what command you have used for blastall? ...
written 9 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by kashifalikhan00740
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fixedStep or variableStep Smoothening wig file
... Is there any tools available for smoothing the wig file (fixed or variable) with different span (wig file can have with any spanned data) ? Although, [DANPOS][1] has a function for smoothing the resultant wig file, but it does not have any separate function for smoothing the wig file. Here I am sh ...
smoothing wiggle wig file written 10 weeks ago by kashifalikhan00740 • updated 10 weeks ago by Alex Reynolds21k

Latest awards to kashifalikhan007

Scholar 10 weeks 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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