Moderator: Goutham Atla

gravatar for Goutham Atla
Goutham Atla7.1k
Reputation:
7,140
Status:
Trusted
Location:
Barcelona/London
Twitter:
geek_y
Last seen:
19 hours ago
Joined:
5 years, 2 months ago
Email:
g***********@gmail.com

Computational Biology. Marie-Curie ESR. Regulatory genomics. Beta-cell biology. 

Posts by Goutham Atla

<prev • 1,166 results • page 1 of 117 • next >
0
votes
1
answer
54
views
1
answers
Comment: C: using DREME and .broadpeak file
... What kind of Chip-Seq data it is ? ...
written 2 days ago by Goutham Atla7.1k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... feautureCounts should do the trick. It has an R interface or command line version. You need to convert your peak coordinates to SAF format as given on their website. ...
written 9 days ago by Goutham Atla7.1k
2
votes
2
answers
226
views
2
answers
Comment: C: Picard vs samtools rmdup
... post exact commands and `samtools flagstat` output before and after removing duplicates ...
written 4 weeks ago by Goutham Atla7.1k
1
vote
0
answers
160
views
0
answers
Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... Its need not be scaling treatment to control always. It scales the sample with large number of reads to sample with smaller number of reads. ...
written 5 weeks ago by Goutham Atla7.1k
1
vote
0
answers
160
views
0
answers
Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... I would pool all control samples and call peaks on each treatment sample independently. macs2 callpeak -t tfile1.bam -c ctrl_pooled.bam ...
written 5 weeks ago by Goutham Atla7.1k
1
vote
1
answer
125
views
1
answers
Answer: A: Effects of some especial non-coding regions
... A quick thing to do is to upload them to [GREAT][1] Other long and complicated strategy is to check if those non-coding regions are a part of any regulatory elements. Data from Roadmap Epigenomics or ENCODE will give you the regulatory regions across multiple tissues. You can intersect your region ...
written 5 weeks ago by Goutham Atla7.1k
1
vote
2
answers
221
views
2
answers
Answer: C: why dont we need technical replicate in case of RNA Seq.?
... I don't think "**RNA seq is new emerging technology**". You don't need technical replicates but you need biological replicates. For allele isoform expression, you need many samples ( as you need to work with genotypes ) with more sequencing depth than that is required for DGE. ...
written 5 weeks ago by Goutham Atla7.1k
1
vote
1
answer
150
views
1
answers
Comment: C: Upstream Regulator Gene Differential expression
... How many replicates do you have ? What does the PCA tells ? Does it clearly separates the WT and KO ? Does the GO of these differential genes agree with the biological function of SOX2 ? Instead of looking for IPA etc, you can do a motif enrichment analysis ( Homer/FIMO etc ) on the promoters/proxim ...
written 5 weeks ago by Goutham Atla7.1k
0
votes
3
answers
200
views
3
answers
Answer: A: Can I run ENCODE ChIP-Seq pipeline or get their code?
... You can definitely run. All the scripts are on github with a detailed protocol. https://github.com/kundajelab/chipseq_pipeline ...
written 8 weeks ago by Goutham Atla7.1k
0
votes
3
answers
213
views
3
answers
Answer: A: CAGE seq & RNA-seq
... Most of the data from CAGE protocol comprised of only 5' end and usually short reads. So you can not use CAGE data to study fusion, unless you have a long read PE CAGE data. CAGE-Seq and RNA-Seq are complimentary to each other in terms of studying the gene expression levels, as long as you have dat ...
written 9 weeks ago by Goutham Atla7.1k

Latest awards to Goutham Atla

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Great Question 11 days ago, created a question with more than 5,000 views. For Understanding Samtools Flagstat Output
Scholar 12 days ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Good Answer 26 days ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Annotation Bed File For Phaseolus Vulgaris
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 3 months ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Popular Question 3 months ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 4 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Popular Question 4 months ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 4 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 5 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 476 users visited in the last hour