Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: sangram_keshari

gravatar for sangram_keshari
Reputation:
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 >
0
votes
1
answer
136
views
1
answers
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_keshari • 30
2
votes
1
answer
136
views
1
answers
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_keshari • 30
0
votes
1
answer
136
views
1
answers
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_keshari • 30
2
votes
1
answer
119
views
1
answers
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_keshari • 30
0
votes
1
answer
136
views
1
answers
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_keshari • 30
0
votes
1
answer
136
views
1
answers
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_keshari • 30
0
votes
2
answers
6.4k
views
2
answers
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_keshari • 30
3
votes
1
answer
136
views
1
answer
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_keshari • 30
2
votes
1
answer
358
views
1
answer
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_keshari • 30 • updated 6 months ago by Kevin Blighe ♦ 21k
0
votes
1
answer
307
views
1
answers
Comment: C: Arabidopsis thaliana whole genome
... I guess Ensemble data also treated as standard?? ...
written 6 months ago by sangram_keshari • 30

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.
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 968 users visited in the last hour