User: sangram_keshari

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

Bioinformatics Student.

Posts by sangram_keshari

<prev • 20 results • page 1 of 2 • next >
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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 16 days 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 16 days 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 17 days 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 weeks ago by sangram_keshari30
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Comment: C: cuffcompare: No novel genes found. Is this possible?
... No, Actually I am comparing my sample transcriptome (GTF) with Annotation file (GFF3 in my case). This supposed to give novel transcripts (As class code: J in output files) which are not reported before in annotation file. ...
written 5 weeks ago by sangram_keshari30
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Comment: C: cuffcompare: No novel genes found. Is this possible?
... Sorry for incomplete information. This is Arabidopsis species. I used the latest version of annotation (GTF guide) from Araport. I have read the documentation of both pipelines (TopHat-Cufflink and HISAT2-Stringtie) from nature protocol. HISAT2 is definitly superior to TopHat in some benchmark rep ...
written 5 weeks ago by sangram_keshari30
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Comment: C: Rna-Seq: Novel Transcripts Found. What Next?
... My personal choice pipeline for Novel transcript ditection: Tophat/STAR (Mapping) -> Cufflinks (Assembly) -> Cuffmerge -> Cuffcompare (To reference genome) [Pubmet][1] Anyway now that updated: HISAT2 -> Stringtie -> gffcompare [Pubmed][2] [1]: https://www.ncbi.nlm.nih.gov/pmc/ ...
written 5 weeks ago by sangram_keshari30
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cuffcompare: No novel genes found. Is this possible?
... I tried to run cuffcompare using cufflink assembled transcript output and an annotation file. I was expecting to some novel transcripts to be found. But it gave this bellow output (stats)? Can anyone help what may have gone wrong? # Cuffcompare v2.2.1 | Command line was: #cuffcompare CLV_ ...
cuffcompare rna-seq written 5 weeks ago by sangram_keshari30
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Compare Microarray with RNA-Seq
... Hello, I am trying to compare the genes of interest which we got through microarray earlier and through RNA-Seq recently. I read couple of papers but they did not give a clear cut idea of how to statistically normalise the expression values so that both can be compared. So, RNASeq expression data ...
microarray rna-seq written 6 months ago by sangram_keshari30 • updated 6 months ago by Kevin Blighe21k
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Comment: C: Arabidopsis thaliana whole genome
... I guess Ensemble data also treated as standard?? ...
written 6 months ago by sangram_keshari30

Latest awards to sangram_keshari

Scholar 16 days ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 5 months ago, voted at least 25 times.
Autobiographer 6 months ago, has more than 80 characters in the information field of the user's profile.

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