User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey1000
Reputation:
1,000
Status:
Trusted
Location:
Karimannoor
Last seen:
4 days, 9 hours ago
Joined:
2 years, 8 months ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 126 results • page 1 of 13 • next >
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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 4 days ago by Jeffin Rockey1000
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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 8 weeks ago by Jeffin Rockey1000
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Comment: C: Bedtools coverage confuses chromosomes
... It should be just that the bed file has mitochondria entry whereas the genome file do not have an entry regarding that. ...
written 8 weeks ago by Jeffin Rockey1000
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Comment: C: Filtering Read Quality - Can remove all reads that have a single read below a th
... single read below a threshold or it is single base (in title)? ...
written 10 weeks ago by Jeffin Rockey1000
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Comment: C: bowtie2-align exited with value 139 ?
... The error 139 related bug that existed before is supposed to be fixed in the bowtie2 version 2.3.4.3 that you are using. However, if you have time to try something which holds a very remote chance of being right, please go back three versions and rerun the same script with bowtie2 v2.3.4 in which a ...
written 11 weeks ago by Jeffin Rockey1000
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Comment: C: samtools sort doesn't finish sorting bam file, just hangs for hours
... Very odd. Command seems fine. If you want to try a different tool use sambamba. ...
written 12 weeks ago by Jeffin Rockey1000
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Comment: C: To obtain upstream DNA sequence by giving location
... Please share the exact flank command used. ...
written 12 weeks ago by Jeffin Rockey1000
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Comment: C: To obtain upstream DNA sequence by giving location
... What is the snippet pasted? ...
written 12 weeks ago by Jeffin Rockey1000
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Comment: C: mapped reads and unmapped reads not equal total number of reads
... Could you please check if counting by reads rather than by pairs is working fine. i.e. Please use flag -F 260 instead of 12 to get mapped count.Also -f 4 instead of 12 to get unmapped. Please add the above two and see if it totals correctly with input count. example samtools view -bhS aln-mt. ...
written 12 weeks ago by Jeffin Rockey1000
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Comment: C: mapped reads and unmapped reads not equal total number of reads
... Could you please share the commands used to calculate mapped & unmapped. And also the aligner used with parameters given. ...
written 12 weeks ago by Jeffin Rockey1000

Latest awards to Jeffin Rockey

Scholar 4 weeks ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 9 weeks ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 11 weeks ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 12 weeks ago, created an answer that has been accepted. For A: parsing through gtf file
Centurion 12 weeks ago, created 100 posts.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Good Answer 10 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 11 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 11 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 18 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 21 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
Scholar 2.4 years ago, created an answer that has been accepted. For A: parsing through gtf file

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