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User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey • 510
Reputation:
510
Status:
Trusted
Location:
Karimannoor
Last seen:
4 hours ago
Joined:
2 years ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 60 results • page 1 of 6 • next >
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Comment: C: #Cufflinks# Can I change the tracking id?
... It should be possible using appropriate gtf having **gene_id Ensembl-Gene-Id;transcript_id Ensembl-Transcript-Id** in the 9th column. i.e. Usually it is the value that comes in the above two fields that becomes the tracking id. ...
written 10 hours ago by Jeffin Rockey • 510
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Comment: C: filter_fasta.py not removing sequences from fastq based on read IDs
... There is also a very useful tool in bbMap for your requirement. In case your issue persists, give a try with *filterbyname.sh* in bbMap suite of tools available at [link][1]. [1]: https://sourceforge.net/projects/bbmap/ ...
written 10 hours ago by Jeffin Rockey • 510
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Comment: C: Relative transcript expression
... Govardhan, STAR is compatible with cufflinks. Please paste an error snippet if you get any so that I may help with it ...
written 17 days ago by Jeffin Rockey • 510
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Answer: A: STAR-RNA Segmentation Fault
... Most likely the genome being small would be the problem. I had encountered seg-fault issue while dealing with very small genomes. Pasted below is a snippet from section 2.2.5 of STAR 2.4 manual. Please see whether setting the parameter as advised would solve the issue. ***Very small genome.*** *Fo ...
written 17 days ago by Jeffin Rockey • 510
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Answer: A: converting .gff file to .gtf
... Few other programs that do the conversion. **genome tools** [http://genometools.org/tools/gt_gff3_to_gtf.html][2] **ea-utils** [https://github.com/ExpressionAnalysis/ea-utils/blob/master/clipper/gff2gtf][1] **pasa** [https://github.com/PASApipeline/PASApipeline/blob/master/misc_utilities/gff ...
written 29 days ago by Jeffin Rockey • 510
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Comment: C: cuffdiff error. IT hangs
... Could you once please try without frag bias correction (-b) and the fasta , something like below and see if it works cuffdiff -p 8 ../../RNA/data2/merged/merged.gtf 1.bam 2.bam 3.bam ...
written 7 weeks ago by Jeffin Rockey • 510
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Comment: C: SAM FLAG for primary alignments, secondary alignments and what's their relations
... Today I came across a blog from Simon Andrews regarding MAPQ scores from different aligners which is quite useful in the context of unique alignment. [Link][1] [1]: https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/ ...
written 3 months ago by Jeffin Rockey • 510
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Answer: A: Find reads that completely cover short sequences
... An approach that I would follow is this. Do the alignment with the aligner of your choice against your short sequences fasta file. Make a bed file with the Sequence name, 0, sequence length, bedtools intersect the above bed and the aligned bam with fraction 1 (100 percent coverage of your regions ...
written 3 months ago by Jeffin Rockey • 510
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Answer: A: [STAR] Why are there so many more mapped reads than unmapped reads in my .sam ou
... Yes, the alignment is unique + multiple loci . Too many loci should not be included. Your bam seems to be truncated or so,most likely while converting from sam. Would you please do that conversion of STAR output bam completely using `samtools view -bhS -o sample.bam sample.sam` and do the countings ...
written 3 months ago by Jeffin Rockey • 510
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Comment: C: [STAR] Why are there so many more mapped reads than unmapped reads in my .sam ou
... You have in fact 93 % alignment. Need more information. Would you please provide the output of the below for checks ? * samtools view -c -F260 sample.bam samtools view -c -F256 sample.bam samtools view -c -f4 sample.bam samtools view -c -F4 sample.bam * ...
written 3 months ago by Jeffin Rockey • 510

Latest awards to Jeffin Rockey

Good Answer 9 weeks 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 3 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 3 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Appreciated 7 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 10 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 13 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
Teacher 15 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
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