User: Jeffin Rockey
Jeffin Rockey • 660
- Reputation:
- 660
- Status:
- Trusted
- Location:
- Karimannoor
- Last seen:
- 13 hours ago
- Joined:
- 2 years, 2 months ago
- Email:
- j***********@hotmail.com
Posts by Jeffin Rockey
<prev
• 81 results •
page 1 of 9 •
next >
0
votes
0
answers
38
views
0
answers
... Few places to look :
Ensembl Plants:
[http://plants.ensembl.org/index.html][1]
Phytozome:
[https://phytozome.jgi.doe.gov/pz/portal.html][2]
NCBI:
[https://www.ncbi.nlm.nih.gov/][3]
GigaDB:
[http://gigadb.org][4]
[1]: http://plants.ensembl.org/index.html
[2]: https://phytozome.jgi.doe.go ...
written 14 days ago by
Jeffin Rockey • 660
0
votes
1
answer
84
views
1
answers
... Apart from gffread,please try the following methods also for conversion. If it is still not working with any, then probably the gff file is not proper. Check the source and verify the correctness.
genome tools
[http://genometools.org/tools/gt_gff3_to_gtf.html][1]
ea-utils
[https://github.com/Exp ...
written 21 days ago by
Jeffin Rockey • 660
0
votes
4
answers
218
views
4
answers
... Thanks for the correction Ram. ...
written 22 days ago by
Jeffin Rockey • 660
1
vote
4
answers
218
views
4
answers
... See this [post][1] and tweak for 300.
[1]: https://www.biostars.org/p/79202/ ...
written 22 days ago by
Jeffin Rockey • 660
2
votes
1
answer
206
views
1
answers
... Hi,
STAR alignment happens in two steps the first time and in one step the subsequent times. Like Tophat, Bowtie etc has index created prior to aligment, so does STAR, but here instead of index file, a whole directory with multiple files will be created whose name will be taken from genome_dir arg ...
written 23 days ago by
Jeffin Rockey • 660
1
vote
1
answer
206
views
1
answers
... Could you please share the commands used for both alignment as well for getting stat from SAM. ...
written 25 days ago by
Jeffin Rockey • 660
0
votes
1
answer
167
views
1
answers
Comment:
C: RNA-seq mapping Reference genome
... Could you elaborate on the draft genome and the other genome (.fa)reference? Usually there will be only one genome, one gtf and one or more fastq files. ...
written 28 days ago by
Jeffin Rockey • 660
1
vote
2
answers
270
views
2
answers
Comment:
C: Problem with Bedtools
... - Please give gff itself as -a in bedtools coverage. From the output shown seems like the command was executed the other way.
- bedtools can work directly with bam for intersect in case it itself is required. ...
written 29 days ago by
Jeffin Rockey • 660
1
vote
2
answers
270
views
2
answers
Comment:
C: Problem with Bedtools
... - Please give gff itself as -a in bedtools coverage. From the output shown seems like the command was executed the other way.
- bedtools can work directly with bam for intersect in case it itself is required. ...
written 29 days ago by
Jeffin Rockey • 660
1
vote
0
answers
30
views
0
answers
... My first time seeing a spam created with SO MUCH effort. ...
written 29 days ago by
Jeffin Rockey • 660
Latest awards to Jeffin Rockey
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Appreciated
9 months ago,
created a post with more than 5 votes.
For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1472 users visited in the last hour