User: prakash

gravatar for prakash
prakash30
Reputation:
30
Status:
New User
Location:
INDIA
Last seen:
1 week, 4 days ago
Joined:
2 years, 2 months ago
Email:
j********@gmail.com

Posts by prakash

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answer
149
views
1
answers
Comment: C: Motif database of choice
... Jaspar and TRANSFAC are used widely I guess.. ...
written 5 weeks ago by prakash30
0
votes
2
answers
373
views
2
answers
Comment: A: Nomalize chip-seq data
... Is your 3 ChIPseq dataset for different factor/histone or same factor/histone in different condition ? ...
written 7 weeks ago by prakash30
1
vote
1
answer
186
views
1
answers
Answer: A: Explanation of BETA output
... Have you put this question in [BETA google group][1] ? [1]: https://groups.google.com/forum/#!forum/cistromebeta ...
written 7 weeks ago by prakash30
1
vote
3
answers
335
views
3
answers
Answer: A: How to find out whether Chip-seq peaks falls within promoter or enhancer region
... use [homer][1], you can define the peaks based on "distance to TSS" column as promoter or enhancer. [1]: http://homer.ucsd.edu/homer/ngs/annotation.html ...
written 7 weeks ago by prakash30
0
votes
2
answers
217
views
2
answers
Answer: A: Cuffnorm: which output file should I use
... genes.fpkm_tracking is the file for genes with its normalized FPKM (fragment per kb per millions of mapped reads) ...
written 7 weeks ago by prakash30
0
votes
1
answer
233
views
1
answers
Comment: C: Samtools rmdup and Piccard Markduplicates
... I have edited my query. ...
written 8 weeks ago by prakash30
0
votes
1
answer
233
views
1
answer
Samtools rmdup and Piccard Markduplicates
... Hello Bio Stars, I have doubt regarding duplicate removal from BAM file. I used two tools "**samtools rmdup**" and **Piccard MarkDuplicates**. I would like to understand why both of the tools remove different amount of duplicate reads. The document says: The **MarkDuplicates** tool works by com ...
alignment next-gen written 8 weeks ago by prakash30 • updated 8 weeks ago by Vijay Lakhujani1.3k
0
votes
1
answer
232
views
1
answers
Comment: C: PCR duplicates in RNASeq
... Thank you geek_y ! So if rmdup is removing duplicates, it indicate that my sample has duplicates. I understand duplicate removal is not an good idea for differential expression study, but is it not necessary to remove for Alternate splicing analysis. ...
written 9 weeks ago by prakash30
3
votes
1
answer
232
views
1
answer
PCR duplicates in RNASeq
... Hello Bio stars, I have small query regarding identification and removal of PCR duplicates from RNASeq data. The Tophat2 alignment stats calculated from samtool flagstat shows that there is no PCR duplicates (below alignment stats), but when I used samtools rmdup , it removes significant amount of ...
forum rna-seq written 9 weeks ago by prakash30 • updated 9 weeks ago by geek_y8.0k
0
votes
0
answers
346
views
0
answers
Different FPKM values for same condition form cufflink
... Hi all, I want to understand why cufflink give different FPKM value for same condition (say A) when comparing with two different condition (say B and C) after analysing separately (A vs B and A vs C). Is it possible to calculate FPKM separately for each condition and then calcualate the fold change ...
rna-seq written 12 months ago by prakash30 • updated 12 months ago by genomax34k

Latest awards to prakash

Popular Question 12 days ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value
Popular Question 8 weeks ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 960 users visited in the last hour