User: Sahel

gravatar for Sahel
Sahel250
Reputation:
250
Status:
Trusted
Location:
CANADA
Last seen:
3 years, 8 months ago
Joined:
6 years, 11 months ago
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s*********@gmail.com

Posts by Sahel

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
... Thanks for the paper. It is really helpful. I just have a question from the paper, which I was hoping you could help me with. They mentioned that they aligned RNA from the novel isoforms to human ORFeome to find functional ORFs. I did not understand how they extracted the cDNA sequences form the Cuf ...
written 5.6 years ago by Sahel250
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Comment: C: Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
... As you are experienced in the field, may I ask a question? Comparing cufflink and Trans-AByss, Trans-AByss has a very nice output format, clearly points to the novel event (ex. skipped exon at some position), and even you can extract the sequence of novel transcripts! However, I could not find this ...
written 5.6 years ago by Sahel250
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Comment: C: Identifying Genes That Express Different Isoforms In Cancer Vs Normal Rna-Seq Da
... Hi JC, I actually took your advice and started to use Tophat/Cufflink a few weeks ago. I have 15 tumor and 5 matched normals (human RNA-seq). Everything works great except Cuffdiff. Right now I am running Cuffdiff on the merge.gtf file of all 20 samples, but it keeps running out of memory and looks ...
written 5.7 years ago by Sahel250
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Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
... Hi All, I am looking for the best approach to predict novel and alternative splicing events from RNA-seq data. I tried to use Cufflink and Trans-AByss so far, however they both have limitations that makes using them difficult. Cufflink requires huge amount of memory and takes weeks to run (And I ha ...
splicing expression rna-seq written 5.7 years ago by Sahel250 • updated 4.7 years ago by Malachi Griffith17k
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Using Cuffdiff With Merged Transcripts (Cuffmerge-Merge.Gtf)
... Hi all, I have 6 tumor and 6 normal RNA-seqs. and I would like to use cuffdiff to find differentially expressed transcripts (specially novel transcripts). So far, I used cufflink and then cuffmerge to merge transcript.cfg files for each condition. so I have two merge.gtf files, one for tumor and ...
rnaseq cuffdiff cuffmerge written 5.7 years ago by Sahel250 • updated 5.7 years ago by Graslevy240
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Finding Novel Splicing Events/Transcripts Using Tophat And Cufflinks
... Hi There, I would like to identify novel splicing events occurring in 4 human paired-end RNA-seq samples. From literature I figured tophat and cufflink can do such thing. So I used Tophat to assemble and Cufflink to find all transcripts. Next I used cuffcompare to identify novel transcripts from k ...
tophat cufflinks written 5.8 years ago by Sahel250 • updated 4.5 years ago by Ann2.2k
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Comment: C: Identifying Genes That Express Different Isoforms In Cancer Vs Normal Rna-Seq Da
... This is great, thank you so much Ahmet :) ...
written 6.4 years ago by Sahel250
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Identifying Genes That Express Different Isoforms In Cancer Vs Normal Rna-Seq Data
... Hi There, I am trying to find genes that express different isoforms in cancer vs normal RNA-seq data. The first thing that came to my mind was to do a differential expression analysis at exon level (I used edgeR for this)... then if I find a gene that express less number of exon compared to the ann ...
splicing expression isoform written 6.4 years ago by Sahel250 • updated 18 months ago by kristoffer.vittingseerup1.0k
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Comment: C: Differential Gene Expression Analysis - Rpkm Vs Readcount
... Thanks, everything is much clear now... ...
written 6.4 years ago by Sahel250
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Differential Gene Expression Analysis - Rpkm Vs Readcount
... Hi There, This is my first time doing a differential expression analysis. I am using edgeR R package to do this analysis. So here is my question: Is it true that higher RPKM values for a gene compared to its contols means more expression of that gene?... also is it correct that if one gene is more ...
gene rpkm expression counts read written 6.4 years ago by Sahel250 • updated 6.4 years ago by Damian Kao15k

Latest awards to Sahel

Appreciated 5.6 years ago, created a post with more than 5 votes. For Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
Great Question 5.6 years ago, created a question with more than 5,000 views. For Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
Great Question 5.6 years ago, created a question with more than 5,000 views. For Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
Good Question 5.6 years ago, asked a question that was upvoted at least 5 times. For Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
Epic Question 5.6 years ago, created a question with more than 10,000 views. For Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Finding Novel Splicing Events/Transcripts Using Tophat And Cufflinks
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis - Rpkm Vs Readcount
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Using Cuffdiff With Merged Transcripts (Cuffmerge-Merge.Gtf)
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Identifying Genes That Express Different Isoforms In Cancer Vs Normal Rna-Seq Data
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
Supporter 5.6 years ago, voted at least 25 times.
Student 5.6 years ago, asked a question with at least 3 up-votes. For Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
Student 5.6 years ago, asked a question with at least 3 up-votes. For Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files

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