User: Vasu

gravatar for Vasu
Vasu410
Reputation:
410
Status:
Trusted
Location:
Last seen:
11 hours ago
Joined:
5 years, 3 months ago
Email:
v**********@gmail.com

Posts by Vasu

<prev • 288 results • page 1 of 29 • next >
0
votes
0
answers
107
views
0
answers
Comment: C: Different miRNAs with same miRNA regions in TCGA
... Ok got the answer from this link [miRNAseq isoform-to-mature miRNA quantification][1] [1]: https://www.biostars.org/p/101182/ ...
written 5 weeks ago by Vasu410
0
votes
0
answers
107
views
0
answers
Comment: C: Different miRNAs with same miRNA regions in TCGA
... In `mirTarbase` hsa-let-7a-5p is the only which has Accession `MIMAT0000062`. I actually want the names of the above table and miRNA target information names to be same. And this can be only based on `miRNA_region`. So, if I treat all the three miRNAs like that it will be same miRNA region for all t ...
written 5 weeks ago by Vasu410
0
votes
0
answers
107
views
0
answers
Different miRNAs with same miRNA regions in TCGA
... I have the miRNA data from TCGA as below: where for three miRNAs have the same mature miRNA region. Should I treat all of them as the same miRNA? I mean can I sum the read counts based on the miRNA region and treat all as single miRNA? miRNA_ID read_count miRNA_region barcode hsa-let-7a-1 ...
mirtarbase tcga mirnaseq mirna written 5 weeks ago by Vasu410
0
votes
1
answer
124
views
1
answers
Comment: C: Question about Isoform expression (miRNA) data from TCGA
... Thanks a lot sudbery. So, now I will sum all the mature 3p and also sum the 5p and exclude precursor and stemloop for the analysis. ...
written 6 weeks ago by Vasu410
3
votes
1
answer
124
views
1
answer
Question about Isoform expression (miRNA) data from TCGA
... I have downloaded the miRNA Isoform expression quantification data (`mirbase21.isoforms.quantification.txt`) from TCGA. The data looks like below: miRNA_ID read_count miRNA_region hsa-let-7b 2 precursor hsa-let-7b 1 precursor hsa-let-7b 1 precursor ...
mirbase mirnaseq tcga mirtarbase mirna written 6 weeks ago by Vasu410 • updated 6 weeks ago by i.sudbery6.2k
1
vote
2
answers
214
views
2
answers
Comment: C: Question about miRNA nomenclature
... Ok. I guess its better to download `mirbase21.isoforms.quantification.txt` data from TCGA which has information about Accession. And then I also used `miRBaseConverter` R package to get the information about mature regions and Accession. This gave all 3p and 5p information. Then I did sum the counts ...
written 6 weeks ago by Vasu410
0
votes
2
answers
214
views
2
answers
Comment: C: Question about miRNA nomenclature
... Small question. I got the target information from [mirTarbase][1] for humans. Almost more than 80% miRNAs are with 5p annd 3p. And the miRNA expression data I downloaded from TCGA Breast which has 1880 miRNAs. In this not even one miRNA is with 5p and 3p. The miRNA names in downloaded TCGA Breast e ...
written 7 weeks ago by Vasu410
0
votes
2
answers
214
views
2
answers
Comment: C: Question about miRNA nomenclature
... sure. thanks a lot for the information ...
written 7 weeks ago by Vasu410
0
votes
2
answers
214
views
2
answers
Comment: C: Question about miRNA nomenclature
... Thank you very much for the clarification. ...
written 7 weeks ago by Vasu410
15
votes
2
answers
214
views
8 follow
2
answers
Question about miRNA nomenclature
... Im working on some analysis with miRNA expression data and miRNA targets information from different sources like miRBase, Targetscan etc... The names of miRNAs in the expression data and miRNAs targets information data need to be same for my analysis But I see that in both of these data, names lo ...
mirbase mirnaseq mirna written 7 weeks ago by Vasu410 • updated 7 weeks ago by i.sudbery6.2k

Latest awards to Vasu

Great Question 3 days ago, created a question with more than 5,000 views. For Sample names for TCGA data from GDC-legacy archive
Student 6 weeks ago, asked a question with at least 3 up-votes. For Sample names for TCGA data from GDC-legacy archive
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For C: Sample names for TCGA data from GDC-legacy archive
Popular Question 4 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 4 months ago, created a question with more than 1,000 views. For cuffdiff for groups
Popular Question 4 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Great Question 6 months ago, created a question with more than 5,000 views. For How to build Hisat2 index for human genome (GRCh37 )?
Popular Question 6 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 8 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 8 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 9 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 9 months ago, created a question with more than 1,000 views. For cuffdiff for groups
Popular Question 11 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 12 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 13 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 13 months ago, created a question with more than 1,000 views. For cuffdiff for groups
Appreciated 13 months ago, created a post with more than 5 votes. For C: Sample names for TCGA data from GDC-legacy archive
Student 13 months ago, asked a question with at least 3 up-votes. For Sample names for TCGA data from GDC-legacy archive
Popular Question 14 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 15 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 15 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 17 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 18 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Voter 18 months ago, voted more than 100 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1227 users visited in the last hour