User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey1.1k
Reputation:
1,120
Status:
Trusted
Location:
Karimannoor
Last seen:
3 weeks, 2 days ago
Joined:
3 years, 10 months ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 134 results • page 1 of 14 • next >
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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],$5,sixth[1]}' df.bed ...
written 7 months ago by Jeffin Rockey1.1k • updated 7 months ago by finswimmer13k
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Comment: C: How to extract filename and change text in the same file
... Hi Ole, Could you please point me to some link or so which would help me understand the {},::: etc. ...
written 12 months ago by Jeffin Rockey1.1k
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Comment: C: Bowtie Index building for wheat genome
... Are you sure the bowtie2-build completed successfully prior to attempting align? *2.bt2l seems to be of 0 size. ...
written 13 months ago by Jeffin Rockey1.1k
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Answer: A: Bowtie Index building for wheat genome
... Install bowtie2 and use *bowtie2-build* to build index. It will automatically build **.bt2l** indices for wheat. ...
written 13 months ago by Jeffin Rockey1.1k
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Comment: C: How to extract filename and change text in the same file
... Hi Malcom, The suggested command appears to be super efficient, even though I did not understand many of the usages. Can you please explain the {=s/.new.vc$f//=}, {}, ::: etc ...
written 13 months ago by Jeffin Rockey1.1k
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Comment: C: How to extract filename and change text in the same file
... Hi Pierre, I did not understand. Would bcftools view do any replacement ? ...
written 13 months ago by Jeffin Rockey1.1k
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Comment: C: How to extract filename and change text in the same file
... Changing ***1s|*** to simply ***s|*** will do replacements for all *Sample1* occurrences. ...
written 13 months ago by Jeffin Rockey1.1k
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Answer: A: How to extract filename and change text in the same file
... In bash this should do. for i in *.new.vcf do ID_NAME=$(basename "$i" .new.vcf) sed -i "1s|Sample1|$ID_NAME|g" $i done Caution: I have used -i with sed. So the actual files will get edited in place. Now added 1s also as to limit the replacement to first line ...
written 13 months ago by Jeffin Rockey1.1k
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Comment: C: ddRAD analysis pipelines
... Stacks issue I could not resolve. ipyrad issue root cause was wrong cut site information given which I corrected. ...
written 13 months ago by Jeffin Rockey1.1k
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Comment: C: Bedtools coverage confuses chromosomes
... Check the separators. MT is there in EHMT1 . Is the bed made in a Windows machine or so? If so dos2unix might help Also what about *GRCh38.dna.primary_assembly.Genome_File.txt* ? ...
written 15 months ago by Jeffin Rockey1.1k

Latest awards to Jeffin Rockey

Popular Question 5 weeks ago, created a question with more than 1,000 views. For ddRAD analysis pipelines
Scholar 5 months ago, created an answer that has been accepted. For A: Cuffflinks installation problem
Supporter 12 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: bedtools getfasta for mm9 genome
Guru 13 months ago, received more than 100 upvotes.
Scholar 13 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 14 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 15 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 16 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 16 months ago, created an answer that has been accepted. For A: parsing through gtf file
Centurion 16 months ago, created 100 posts.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Good Answer 23 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
Scholar 2.1 years ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 2.1 years ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 2.6 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 2.9 years ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 3.0 years ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 3.6 years ago, created an answer that has been accepted. For A: parsing through gtf file

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