User: cschu181
cschu181 • 1.7k
- Reputation:
- 1,700
- Status:
- Trusted
- Location:
- Last seen:
- 1 day, 11 hours ago
- Joined:
- 5 years, 10 months ago
- Email:
- c********@gmail.com
about me
Posts by cschu181
<prev
• 282 results •
page 1 of 29 •
next >
3
votes
1
answer
96
views
1
answers
... I'd say this is expected. Since you're only using short reads your contigs/scaffolds cannot bridge certain low complexity, repetitive regions, so the assembly process will introduce stretches of N where assembly paths cannot be uniquely resolved. I wouldn't worry about this. ...
written 16 days ago by
cschu181 • 1.7k
2
votes
1
answer
135
views
1
answers
Comment:
C: STAR on Galaxy
... Memory is not storage. How much RAM do you have available in your instance? STAR is kinda known to need a lot of that. ...
written 6 weeks ago by
cschu181 • 1.7k
4
votes
1
answer
175
views
1
answers
... awk -v OFS="\t" -v FS="\t" '{ $2=gensub("^mRNA.", "", 0, $2); print $0; }' your_file > your_modified_file
Edit: removed tab-separated assumption, as I just saw it should treat a gtf, which we all know is tab-separated. ...
written 7 weeks ago by
cschu181 • 1.7k
0
votes
0
answers
133
views
0
answers
Comment:
C: Trinity assembly file
... For the second question:
awk '{ print $1; }' Trinity.fasta ...
written 9 weeks ago by
cschu181 • 1.7k
2
votes
2
answers
605
views
2
answers
... What does "local contract" mean? I assume that means non-remote/office-based? ...
written 9 weeks ago by
cschu181 • 1.7k
0
votes
0
answers
178
views
0
answers
... It seems you're using the wrong scores:
if x==0:
f1=float("-inf")
**f2=matrix[i-1][x]**
f3=float("-inf")
elif i==0:
f1=float("-inf")
f2=float("-inf")
**f3=matrix[i][x-1]**
...
written 10 weeks ago by
cschu181 • 1.7k
0
votes
1
answer
181
views
1
answers
... Is there any reason that the gaps need to be translated? There is no gap in the actual sequence, so tt-aaaatg would have a frameshift in relation to tttaaaatg and code for LK instead of FKM.
Just for the sake of it, you could try to see what the biopython translation engine does with "N" in nuclei ...
written 11 weeks ago by
cschu181 • 1.7k
0
votes
0
answers
228
views
0
answers
... Find the ORFs in your transcripts (e.g. with transdecoder) and then blastx (or translate and blastp) against a bacterial protein database. Transcripts without ORFs and those without hits you could process with RNA finding tools (tRNAscan, Infernal, SortmeRNA etc.) and blastn against ncRNA databases. ...
written 12 weeks ago by
cschu181 • 1.7k
1
vote
1
answer
299
views
1
answers
Comment:
C: Folding RNA on python
... Have you looked at [RNAsketch][1]? This is a Python wrapper for the Vienna Package, which might give you just what you want.
[1]: https://github.com/ViennaRNA/RNAsketch ...
written 3 months ago by
cschu181 • 1.7k
0
votes
0
answers
166
views
0
answers
... Align the reads from your samples against the contig. Then you can either visually check the bam files in a browser (IGV etc.) or probe the position with some naive variant calling, e.g samtools mpileup. ...
written 3 months ago by
cschu181 • 1.7k
Latest awards to cschu181
Teacher
16 days ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Good Answer
11 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Getting PFAM database
Scholar
3 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Scholar
11 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: Why bioinformaticians need to know programming languages?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Scholar
14 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Supporter
14 months ago,
voted at least 25 times.
Guru
14 months ago,
received more than 100 upvotes.
Scholar
15 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Commentator
16 months ago,
created a comment with at least 3 up-votes.
For C: Why bioinformaticians need to know programming languages?
Scholar
16 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Scholar
16 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Scholar
17 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Scholar
18 months ago,
created an answer that has been accepted.
For A: Simple python script to convert ambiguity codes
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: Simple python script to convert ambiguity codes
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 615 users visited in the last hour