User: Jeffin Rockey

gravatar for Jeffin Rockey
Jeffin Rockey660
Reputation:
660
Status:
Trusted
Location:
Karimannoor
Last seen:
13 hours ago
Joined:
2 years, 2 months ago
Email:
j***********@hotmail.com

Posts by Jeffin Rockey

<prev • 81 results • page 1 of 9 • next >
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Comment: C: Is there any fully annotated transcriptome reference genome in .gbk and with gff
... Few places to look : Ensembl Plants: [http://plants.ensembl.org/index.html][1] Phytozome: [https://phytozome.jgi.doe.gov/pz/portal.html][2] NCBI: [https://www.ncbi.nlm.nih.gov/][3] GigaDB: [http://gigadb.org][4] [1]: http://plants.ensembl.org/index.html [2]: https://phytozome.jgi.doe.go ...
written 14 days ago by Jeffin Rockey660
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Answer: A: gffread error when converting gff to gtf
... Apart from gffread,please try the following methods also for conversion. If it is still not working with any, then probably the gff file is not proper. Check the source and verify the correctness. genome tools [http://genometools.org/tools/gt_gff3_to_gtf.html][1] ea-utils [https://github.com/Exp ...
written 21 days ago by Jeffin Rockey660
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Comment: C: Remove sequences <300 bases from FASTA file
... Thanks for the correction Ram. ...
written 22 days ago by Jeffin Rockey660
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Comment: A: Remove sequences <300 bases from FASTA file
... See this [post][1] and tweak for 300. [1]: https://www.biostars.org/p/79202/ ...
written 22 days ago by Jeffin Rockey660
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Comment: C: Low alignment with Trinity but high alignment in SAM files
... Hi, STAR alignment happens in two steps the first time and in one step the subsequent times. Like Tophat, Bowtie etc has index created prior to aligment, so does STAR, but here instead of index file, a whole directory with multiple files will be created whose name will be taken from genome_dir arg ...
written 23 days ago by Jeffin Rockey660
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Comment: C: Low alignment with Trinity but high alignment in SAM files
... Could you please share the commands used for both alignment as well for getting stat from SAM. ...
written 25 days ago by Jeffin Rockey660
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Comment: C: RNA-seq mapping Reference genome
... Could you elaborate on the draft genome and the other genome (.fa)reference? Usually there will be only one genome, one gtf and one or more fastq files. ...
written 28 days ago by Jeffin Rockey660
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Comment: C: Problem with Bedtools
... - Please give gff itself as -a in bedtools coverage. From the output shown seems like the command was executed the other way. - bedtools can work directly with bam for intersect in case it itself is required. ...
written 29 days ago by Jeffin Rockey660
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Comment: C: Problem with Bedtools
... - Please give gff itself as -a in bedtools coverage. From the output shown seems like the command was executed the other way. - bedtools can work directly with bam for intersect in case it itself is required. ...
written 29 days ago by Jeffin Rockey660
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Comment: C: Job: Assistant Teacher of Bioinformatics and Computational Biology, New York Uni
... My first time seeing a spam created with SO MUCH effort. ...
written 29 days ago by Jeffin Rockey660

Latest awards to Jeffin Rockey

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Good Answer 4 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 5 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 5 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 12 months ago, created an answer that has been accepted. For A: parsing through gtf file
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Faster way to get coverage per base
Scholar 15 months ago, created an answer that has been accepted. For A: parsing through gtf file
Scholar 17 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 23 months ago, created an answer that has been accepted. For A: parsing through gtf file

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