User: Govardhan Anande

Reputation:
130
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Trusted
Location:
Australia
Last seen:
7 months, 1 week ago
Joined:
4 years, 6 months ago
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Posts by Govardhan Anande

<prev • 47 results • page 1 of 5 • next >
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130
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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 13 months ago by Govardhan Anande130 • updated 13 months ago by WouterDeCoster40k
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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 2.1 years ago by Govardhan Anande130 • updated 3 months ago by zhaoliang03020
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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 2.6 years ago by Govardhan Anande130

Latest awards to Govardhan Anande

Popular Question 12 months ago, created a question with more than 1,000 views. For splice junction file for human(hg19)
Popular Question 12 months ago, created a question with more than 1,000 views. For Correlation cluster map in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Correlation cluster map in R
Popular Question 14 months ago, created a question with more than 1,000 views. For Correlation cluster map in R
Popular Question 15 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 2.6 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 2.7 years ago, created a question with more than 1,000 views. For Why there is huge difference in mapping quality with bwa & bowtie

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