User: waqaskhokhar999
waqaskhokhar999 • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- Last seen:
- 3 months ago
- Joined:
- 8 years, 2 months ago
- Email:
- w**************@gmail.com
about me
Posts by waqaskhokhar999
<prev
• 85 results •
page 1 of 9 •
next >
0
votes
0
answers
689
views
0
answers
... I have manhattan plots for each trait but is there any way by which I can plot manhattan plot for all traits together to see the p-value distribution ...
written 3 months ago by
waqaskhokhar999 • 100
0
votes
0
answers
689
views
0
answers
... I have ploted the qq plot for all traits together but it depeicts expected vs actual p-values and the graph is not very much clear that's why i am trying to look for other options ...
written 3 months ago by
waqaskhokhar999 • 100
0
votes
0
answers
689
views
0
answers
... I have 10,000 SNPs and 48 different phenotypic traits, so I performed GWAS based on Mixed Linear Model (MLM) approach using Tassel. I have got associations and now I am interested to see the distribution of p values to better [interpret p-values][1] so I extracted the p-values for all traits from t ...
written 3 months ago by
waqaskhokhar999 • 100
1
vote
1
answer
173
views
1
answer
... I have a large tab-delimited file and a part of it is like:
25 M X A A X S
25_a M K A A R S
25_b M A A A V S
31 M A A A V S
31_a M A A A V S
31_b M A A A V S
I am trying to play with three rows at a time, the first row contains a reference sequence (actual sequence ...
written 9 months ago by
waqaskhokhar999 • 100
• updated
9 months ago by
JC ♦ 12k
1
vote
0
answers
186
views
0
answers
... I have three fasta files reflecting protein sequences for each gene in xls format (space separated). The first column contains header, while the other column contains sequence. For example:
File1:
sample 1 2 3 4 5 6
BnaA03g18710D M A A A V S
BnaA03g18710D_S25 M A A A V S
BnaA03g187 ...
written 10 months ago by
waqaskhokhar999 • 100
0
votes
1
answer
253
views
1
answers
... Many thanks for this guidance, I have tried to work on regex but didn't get success, So I thought instead of finding the nucleotide sequence for ambiguous codon, I can start with CDS sequence that is coding for those codons and can sort out the ambiguous nucleotide. I understand the first point but ...
written 10 months ago by
waqaskhokhar999 • 100
3
votes
1
answer
253
views
1
answer
... I have multi fasta nucleotide file, I am interested to replace the [ambigious nucleotides][1] (R, Y, S, K, e.t.c) with a possible combination of nucleotides and save both options. For example, the following nucleotide sequence (sudo example):
>Seq1
ATGGKCRCCGCSGT
Contain ambiguous nucle ...
written 10 months ago by
waqaskhokhar999 • 100
• updated
10 months ago by
_r_am ♦ 32k
0
votes
1
answer
292
views
1
answers
... I would like to keep both combinations, in the sequence a the yag will become cag and codes for Q, while in the sequence b the yag will become tag and reflects stop codon (*) and the outputs would be like these:
>ORF1_BnaA03g18710D_S45:82:1509_a
MAAAVSTVGAINRAPLSLNGSGAGAASVPATTFLGKKVVTAS ...
written 10 months ago by
waqaskhokhar999 • 100
• updated
10 months ago by
_r_am ♦ 32k
2
votes
1
answer
292
views
1
answer
... I have two multi-fasta files, one contains nucleotide sequences, and a subset of nucleotide sequence for ORF1 is:
>ORF1_BnaA03g18710D_S45:82:1509
ATGGCCGCCGCAGTTTCCACCGTCGGTGCCATCAACAGAGCTCCGTTGAGCTTGAACGGG
TCAGGAGCAGGAGCTGCTTCAGTCCCAGCTACGACCTTCTTGGGAAAGAAAGTTGTAACC
GCGTCGAGATTC ...
written 10 months ago by
waqaskhokhar999 • 100
• updated
10 months ago by
Asaf ♦ 8.5k
0
votes
5
answers
10k
views
5
answers
Comment:
C: How to extract the longest orf?
... Can you please tell me how I can use get_longest_ORF_per_transcript.pl script, I have tried following command:
perl TransDecoder-TransDecoder-v5.5.0/util/get_longest_ORF_per_transcript.pl input_file
But got this error:
Error, cannot parse header info: BnaA03g18710D_ref at TransDecoder-TransDeco ...
written 10 months ago by
waqaskhokhar999 • 100
Latest awards to waqaskhokhar999
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Alternative splicing events in transcriptomic data
Popular Question
9 months ago,
created a question with more than 1,000 views.
For strandness of paired-end data
Supporter
11 months ago,
voted at least 25 times.
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Alternative splicing events in transcriptomic data
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1158 users visited in the last hour