User: kashifalikhan007

Reputation:
40
Status:
New User
Location:
Cologne
Last seen:
10 hours ago
Joined:
3 years, 3 months ago
Email:
k***************@gmail.com

Posts by kashifalikhan007

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answer
132
views
1
answers
Comment: C: MCScanX result problem
... what command you have used for blastall? ...
written 22 hours ago by kashifalikhan00740
0
votes
0
answers
104
views
0
answers
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 7 days ago by kashifalikhan00740
0
votes
1
answer
132
views
1
answers
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 7 days ago by kashifalikhan00740
1
vote
5
answers
224
views
5
answers
Answer: A: chrom.sizes computed locally
... Try samtools samtools faidx genome.fa cut -f1,2 genome.fa.fai > genome.size ...
written 7 days ago by kashifalikhan00740
2
votes
1
answer
121
views
1
answers
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 7 days ago by kashifalikhan00740
0
votes
1
answer
132
views
1
answers
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 7 days ago by kashifalikhan00740
0
votes
2
answers
131
views
2
answers
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 7 days ago by kashifalikhan00740
3
votes
2
answers
113
views
2
answers
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 8 days ago by kashifalikhan00740 • updated 7 days ago by Alex Reynolds20k
0
votes
1
answer
4.8k
views
1
answers
Comment: C: Converstion of BED with scores into bigWig
... samtools faidx genome.fasta cut -f1,2 genome.fasta.fai > genome.size ...
written 8 days ago by kashifalikhan00740
0
votes
3
answers
7.1k
views
3
answers
Answer: A: Mismatch Option In Bowtie2
... Ashutosh Filtering through XM tag for single end read is OK, but in case of pair-end I have a confusion because both pairs might have different number of mismatches and in this way one can miss a pair in all such cases.   ...
written 19 months ago by kashifalikhan00740

Latest awards to kashifalikhan007

Scholar 7 days 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1393 users visited in the last hour