User: sangram_keshari

Reputation:
30
Status:
New User
Location:
Pondicherry University
Website:
http://sksahu.net/
Twitter:
sangram_ksahu
Last seen:
4 days, 17 hours ago
Joined:
1 year, 7 months ago
Email:
s************@gmail.com

Bioinformatics Student.

Posts by sangram_keshari

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Converting fasta to gtf using reference genome
... If you not sure how to run hisat2 -> this [nature protocol paper][1] can be a good read. [1]: https://www.nature.com/articles/nprot.2016.095 ...
written 27 days ago by sangram_keshari30
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Answer: A: chromosome coordinate, rs
... If you talking about chromosome coordinates. You can either get from GTF file or a BED file for the species you working, depending upon if they are completely sequenced and annotated or not. ...
written 27 days ago by sangram_keshari30
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Comment: C: gffread with wrong output
... After doing this step also, It's giving some similar kind of results. I tried to understand hard why, but couldn't. So I took a different approach with bed tool after filtration setup to get the sequence of each exon of transcripts and some python script to combine them. Its rather complicated, but ...
written 9 weeks ago by sangram_keshari30
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Comment: C: gffread with wrong output
... Sure, Few lines from GTF file (intergenic.gtf) 1 Cufflinks exon 1477451 1477950 0 - 0 gene_id "XLOC_004355" transcript_id "TCONS_00012049" exon_number "1" oId "CUFF.237.1" class_code "u" tss_id "TSS5794" 1 Cufflinks exon 1478389 1478918 0 - 0 gene_id "XLOC_004355" transcript_id "TCON ...
written 9 weeks ago by sangram_keshari30
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gffread with wrong output
... I am trying to get FASTA sequence from a GTF file having transcripts with multiple exons (filtered from merged_transcripts.gtf from cufflink pipeline. To be precise with class_code "u") So I am using **gffread** using this filtered GTF file and the genome file to get the sequence for those transcri ...
assembly sequence rna-seq written 9 weeks ago by sangram_keshari30
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Comment: C: P-value calculation for Gene Ontology Terms
... I hope this might help - https://onlinecourses.science.psu.edu/statprogram/node/138/ They explained with an example. Also, you can also check this previous thread discussion - https://www.biostars.org/p/103894 ...
written 10 weeks ago by sangram_keshari30
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Comment: C: cuffcompare: No novel genes found. Is this possible?
... Yes, The mistake was in Assembly step. Use of reference annotation file as a guide instead of just used for quantifying known transcripts. Thanks for the help :) ...
written 3 months ago by sangram_keshari30
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Answer: A: cuffcompare: No novel genes found. Is this possible?
... Okay, that was a very novice kind mistake on my side. Now that I figured it out. Just let me share it here, in case if someone faces the same. It was in the assembly step (Using Cufflink), that I used the option **-G/--GTF** (*which simply quantitating against reference transcript annotations*) ins ...
written 3 months ago by sangram_keshari30
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Comment: C: cuffcompare: No novel genes found. Is this possible?
... I used STAR for mapping and it was successful with more than 85% reads align to reference genome. ...
written 3 months ago by sangram_keshari30
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Answer: A: SRA toolkit (NCBI) - sra to fasta
... You can use the same utility **fastq-dump** from SRA toolkit to convert from ***.SAR*** to either ***.fastq*** or ***.fasta***. fastq-dump --split-files --fasta 60 SRR390728 This above command will produce two (--split-files) fasta files (--fasta) with 60 bases per line ("60" included after -- ...
written 4 months ago by sangram_keshari30

Latest awards to sangram_keshari

Scholar 3 months ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 8 months ago, voted at least 25 times.
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.

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