User: sangram_keshari
sangram_keshari • 30
- Reputation:
- 30
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- Location:
- Pondicherry University
- Website:
- http://sksahu.net/
- Twitter:
- sangram_ksahu
- Last seen:
- 4 days, 17 hours ago
- Joined:
- 1 year, 7 months ago
- Email:
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Bioinformatics Student.
Posts by sangram_keshari
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... 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_keshari • 30
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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_keshari • 30
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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_keshari • 30
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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_keshari • 30
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... 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 ...
written 9 weeks ago by
sangram_keshari • 30
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... 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_keshari • 30
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... 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_keshari • 30
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... 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_keshari • 30
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... I used STAR for mapping and it was successful with more than 85% reads align to reference genome. ...
written 3 months ago by
sangram_keshari • 30
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... 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_keshari • 30
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?
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