User: Govardhan Anande

Reputation:
130
Status:
Trusted
Location:
Australia
Last seen:
3 months ago
Joined:
4 years, 2 months ago
Email:
g*************@gmail.com

Posts by Govardhan Anande

<prev • 47 results • page 1 of 5 • next >
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... I have MISO results and as you know miso only consider alternative exon along with upstream and downstream exons but not entire transcript. ...
written 9 months ago by Govardhan Anande130
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... Jeffin, you are right cufflinks accepts the STAR bam files but results are different. I tried feeding one sample bam from TopHat and STAR. Anyways, I got splicing information from various tool and now I am planning use that value. I posted this question here because I wish to compare entire trans ...
written 9 months ago by Govardhan Anande130
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... Again, the problem with RSEM is the alignment. I have bam files from STAR and they are not compatible with RSEM and same goes for cufflinks as well. Honestly I can't afford realignment so trying to find way to utilise what I have at the moment. Anyways, thank you for your help and time. ...
written 9 months ago by Govardhan Anande130
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... I am working on Human samples, so I just need expression of each transcripts from one gene. Thanks, Govardhan ...
written 9 months ago by Govardhan Anande130
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... Why do I need to use reference GTF when I can use gtf of two transcripts?? Is it something StrinTie requires?? and output of above command is GTF i.e. `chrM StringTie transcript 1 16571 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "20872.708984"; ch ...
written 9 months ago by Govardhan Anande130
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... Alignment STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --runThreadN 10 --genomeDir $FastaIndex --readFilesIn $R1 $R2 I just started with basic one for abundance ~/stringtie-1.3.4d.Linux_x86_64/stringtie Aligned.sortedByCoord.out.bam -G Demo.gtf ...
written 9 months ago by Govardhan Anande130
0
votes
3
answers
437
views
3
answers
Comment: C: Relative transcript expression
... Hi Vijay, Thank you. Yes, I have identified the transcripts and I have generated GTF file of two transcripts. Now I am trying to get the relative abundance but I getting "Error: could not any valid reference transcripts in Demo.gtf (invalid GTF/GFF file?)? My gtf looks like : `chrX protein_ ...
written 9 months ago by Govardhan Anande130
3
votes
3
answers
437
views
6 follow
3
answers
Relative transcript expression
... Hi, I have been trying to understand relative expression of two transcripts from a gene. Let's, say I have a gene with 6 exon and it produces two transcripts: isoform 1 with all 6 exons. and isoform 2 with exon 1, 2, 3, 4 & 6. I have bam files STAR and I don't want to do alignment again s ...
transcript expression rna-seq isoform written 9 months ago by Govardhan Anande130 • updated 9 months ago by WouterDeCoster37k
0
votes
0
answers
649
views
0
answers
Gene expression based risk score
... Hello, I have identified 11 prognostic genes using LASSO Cox model using 200 samples (https://web.stanford.edu/~hastie/Papers/Glmnet_Vignette.pdf). Now I would like to calculate risk score to every sample based on expression of these 11 prognostic genes and I would really appreciate if anyone can ...
sequencing gene expression rna-seq risk score written 21 months ago by Govardhan Anande130
0
votes
2
answers
11k
views
2
answers
Comment: C: How To Create A Venn Diagram Of Sample1.Vcf, Sample2.Vcf And Sample1&2(Union).Vc
... Did anyone figured it out for three vcf files??? ...
written 2.3 years ago by Govardhan Anande130

Latest awards to Govardhan Anande

Popular Question 8 months ago, created a question with more than 1,000 views. For splice junction file for human(hg19)
Popular Question 8 months ago, created a question with more than 1,000 views. For Correlation cluster map in R
Popular Question 9 months ago, created a question with more than 1,000 views. For Correlation cluster map in R
Popular Question 10 months ago, created a question with more than 1,000 views. For Correlation cluster map in R
Popular Question 11 months ago, created a question with more than 1,000 views. For Any Promising Addition to Alternative Splicing Detection tools for Rna-Seq Data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Why there is huge difference in mapping quality with bwa & bowtie
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Why there is huge difference in mapping quality with bwa & bowtie

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1033 users visited in the last hour