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User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey • 990
Reputation:
990
Status:
Trusted
Location:
Karimannoor
Last seen:
1 day ago
Joined:
2 years, 6 months ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 123 results • page 1 of 13 • next >
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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 7 days ago by Jeffin Rockey • 990
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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 17 days ago by Jeffin Rockey • 990
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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 21 days ago by Jeffin Rockey • 990
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Comment: C: To obtain upstream DNA sequence by giving location
... Please share the exact flank command used. ...
written 21 days ago by Jeffin Rockey • 990
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Comment: C: To obtain upstream DNA sequence by giving location
... What is the snippet pasted? ...
written 21 days ago by Jeffin Rockey • 990
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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 22 days ago by Jeffin Rockey • 990
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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 22 days ago by Jeffin Rockey • 990
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Comment: C: tophat running does not complete properly.
... OK. What is the **genome** given in the command line? tophat -p 8 -G genome.gtf -o sample_thout **genome** SAMPLE_R1.fq SAMPLE_R2.fq ...
written 22 days ago by Jeffin Rockey • 990
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Comment: C: To obtain upstream DNA sequence by giving location
... The file required is ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz . Please download and run the script. ...
written 22 days ago by Jeffin Rockey • 990
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Comment: C: bowtie2-align died with signal 6 (ABRT) (core dumped)
... Also, are you using some very old version of bowtie2. Please specify the bowtie2 version. ...
written 22 days ago by Jeffin Rockey • 990

Latest awards to Jeffin Rockey

Scholar 2 days ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 20 days ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 22 days ago, created an answer that has been accepted. For A: parsing through gtf file
Centurion 23 days ago, created 100 posts.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Good Answer 8 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 9 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 9 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Appreciated 13 months ago, created a post with more than 5 votes. For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Scholar 16 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 17 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
Scholar 20 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 2.3 years ago, created an answer that has been accepted. For A: parsing through gtf file
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