User: Ron
Ron • 600
- Reputation:
- 600
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 1 week ago
- Joined:
- 3 years, 9 months ago
- Email:
- r*********@yahoo.co.in
about me
Posts by Ron
<prev
• 288 results •
page 1 of 29 •
next >
0
votes
5
answers
818
views
5
answers
... I used RseQC for rRNA detection.
They have a bed file too.
http://rseqc.sourceforge.net/
...
written 9 days ago by
Ron • 600
0
votes
0
answers
162
views
0
answers
Comment:
C: HtSeq count error
... No,I had to revert back to the older version.The newer version still giving me the issue.
I think BAM file needs to be modified,in order to get it working with the newer version. ...
written 28 days ago by
Ron • 600
0
votes
0
answers
162
views
0
answers
Comment:
A: HtSeq count error
... The bam file is working fine with older HTSEQ version 0.6.1, which I was using previously.
So I reverted back. ...
written 29 days ago by
Ron • 600
0
votes
0
answers
110
views
0
answers
... Can you explain more on the continuous outcome? ...
written 29 days ago by
Ron • 600
0
votes
3
answers
155
views
3
answers
... GDC has cancer data processed.
There are 11k samples.
https://portal.gdc.cancer.gov/ ...
written 29 days ago by
Ron • 600
0
votes
4
answers
228
views
4
answers
... You can do pathway enrichment using GSEA
http://software.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html
GSEA pre-ranked requires complete list of genes with fold changes.
you can chose signatures of interest and see if they are enriched. ...
written 29 days ago by
Ron • 600
0
votes
0
answers
162
views
0
answers
... Hi all,
I updated to new htseq count and am getting these errors.
I was using previous version 0.6.1 and it was working well.
Error occured when reading beginning of SAM/BAM file.
'pysam.csamtools.AlignedRead' object has no attribute 'reference_start'
[Exception type: AttributeError, raised in ...
written 29 days ago by
Ron • 600
0
votes
3
answers
234
views
3
answers
... Post alignment ,you can use rseqc, http://rseqc.sourceforge.net/
It has very good modules,to work with BAM.
Also ,if you use STAR for alignment,please look out the log.final.out file for QC metrics. ...
written 29 days ago by
Ron • 600
0
votes
1
answer
134
views
1
answers
Comment:
C: Xenopus genome files for RNAseq
... Try checking the links I pasted above.These are xenbase links only. ...
written 29 days ago by
Ron • 600
0
votes
1
answer
134
views
1
answers
... I would use this file for the X. laevis 9.1 genome https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.xenbase.org_pub_Genomics_JGI_Xenla9.1_Xla.v91.repeatMasked.fa.gz&d=DwMFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=pt2eBGtCyE_Qi6slO5RVtfGA3zOwk4_M88OXcU9-nJI&m=kUg0RuM_AE ...
written 4 weeks ago by
Ron • 600
Latest awards to Ron
Popular Question
13 days ago,
created a question with more than 1,000 views.
For Working with human database in Kraken
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For Database of Ligand and receptor genes
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For Database of Ligand and receptor genes
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Database of Ligand and receptor genes
Student
4 months ago,
asked a question with at least 3 up-votes.
For GSEA Preranked analysis on RNA-SEQ
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Great Question
7 months ago,
created a question with more than 5,000 views.
For GSEA Preranked analysis on RNA-SEQ
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Rare Variants From Annotated Vcf File
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Rank Genes By FPKM for only One Sample
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Rank Genes By FPKM for only One Sample
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Cufflinks output with filename prefix
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Clustering of genes using FPKM
Popular Question
16 months ago,
created a question with more than 1,000 views.
For htseq-count for RNA Seq
Centurion
16 months ago,
created 100 posts.
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Extracting reads from multiple regions
Student
19 months ago,
asked a question with at least 3 up-votes.
For GSEA Preranked analysis on RNA-SEQ
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 756 users visited in the last hour