User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey1.1k
Reputation:
1,150
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Trusted
Location:
Karimannoor
Last seen:
2 weeks, 2 days ago
Joined:
4 years, 5 months ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 140 results • page 1 of 14 • next >
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Comment: A: inclusion or exclusion in gff by list of chromosomes/scaffolds
... [@Juke34][1] Thank you. I was looking for such a straight forward way indeed. [1]: https://www.biostars.org/u/12371/ ...
written 10 weeks ago by Jeffin Rockey1.1k
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Comment: C: inclusion or exclusion in gff by list of chromosomes/scaffolds
... Thanks. That should work. ...
written 10 weeks ago by Jeffin Rockey1.1k
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Comment: C: inclusion or exclusion in gff by list of chromosomes/scaffolds
... In fact AGAT was the first place I looked for, for the requirement. That particular script seemed to be based on 9th column. Whereas, the requirement is on the first colum, which infact should be much simpler. But unfortunately I still could not land on the correct tool for the purpose. ...
written 10 weeks ago by Jeffin Rockey1.1k
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inclusion or exclusion in gff by list of chromosomes/scaffolds
... There is a genome fasta file having say 10 chromosomes and 1000 scaffolds. After gene prediction there are genes/mRNA/cds etc prediction in chromosomes as well as scaffolds. Now, a particular requirement is to get genome fasta as well as gff corresponding to chromosomes alone. For genome , the be ...
gff written 10 weeks ago by Jeffin Rockey1.1k
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Comment: C: Change the field separator
... sed is a very handy utility which would be there is many of the unix/linux flavours. s stands for substitute. The | (pipes) act as separators. And it need not be | always. You may as well write like sed `'s/\//,/g'` (I am pretty sure it would confuse more, and hence the pipes) \/ kind of says to ...
written 4 months ago by Jeffin Rockey1.1k
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Answer: A: Change the field separator
... sed 's|\/|,|g' ...
written 4 months ago by Jeffin Rockey1.1k
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Answer: A: How to remove all characters after a specific pattern?
... awk -F$'\t' -v OFS="\t" '{split($4,fourth,":");split($6,sixth,":");print $1,$2,$3,fourth[1],$5,sixth[1]}' df.bed ...
written 14 months ago by Jeffin Rockey1.1k • updated 14 months ago by finswimmer13k
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Comment: C: How to extract filename and change text in the same file
... Hi Ole, Could you please point me to some link or so which would help me understand the {},::: etc. ...
written 19 months ago by Jeffin Rockey1.1k
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Comment: C: Bowtie Index building for wheat genome
... Are you sure the bowtie2-build completed successfully prior to attempting align? *2.bt2l seems to be of 0 size. ...
written 19 months ago by Jeffin Rockey1.1k
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Answer: A: Bowtie Index building for wheat genome
... Install bowtie2 and use *bowtie2-build* to build index. It will automatically build **.bt2l** indices for wheat. ...
written 19 months ago by Jeffin Rockey1.1k

Latest awards to Jeffin Rockey

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Bedtools intersect alternatives available
Popular Question 8 months ago, created a question with more than 1,000 views. For ddRAD analysis pipelines
Scholar 12 months ago, created an answer that has been accepted. For A: Cuffflinks installation problem
Supporter 19 months ago, voted at least 25 times.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: bedtools getfasta for mm9 genome
Guru 20 months ago, received more than 100 upvotes.
Scholar 20 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 21 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 22 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 23 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 23 months ago, created an answer that has been accepted. For A: parsing through gtf file
Centurion 23 months ago, created 100 posts.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Good Answer 2.5 years 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
Scholar 2.6 years ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 2.7 years ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 3.2 years ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 3.4 years ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 3.6 years ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base

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