SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 28
Search took 0.00 seconds.
Search: Posts Made By: vkartha
Forum: Bioinformatics 08-05-2014, 09:12 AM
Replies: 6
Views: 2,842
Posted By vkartha
On a similar note - I am trying to perform...

On a similar note - I am trying to perform differential expression contrasts for 2 different populations - one resistant to a given drug and one wild type (i.e. sensitive). Within each population, I...
Forum: Bioinformatics 07-02-2014, 11:17 AM
Replies: 5
Views: 2,698
Posted By vkartha
Thanks for your reply! I actually did try adding...

Thanks for your reply! I actually did try adding the batch term as a covariate to the design model specification in both edgeR and DESeq2 but I see very few DE genes (10-20 out of 20,000 tested)...
Forum: Bioinformatics 07-02-2014, 06:46 AM
Replies: 5
Views: 2,698
Posted By vkartha
Hi - I have a question related to 'manually'...

Hi - I have a question related to 'manually' adjusting for batch effects using RNASeq data (and by manually I mean not using built in batch adjustment from packages like edgeR and DESeq2, but using...
Forum: Introductions 06-08-2014, 09:33 AM
Replies: 6
Views: 4,107
Posted By vkartha
I was trying to process some paired-end RNASeq...

I was trying to process some paired-end RNASeq data and attempted to use the latest version of htseq (0.6.1). For some reason, it doesn't make it past a certain record complaining about expecting...
Forum: RNA Sequencing 05-29-2014, 07:28 AM
Replies: 8
Views: 2,692
Posted By vkartha
Hi, Using Tophat v 2.0.11 for my paired-end...

Hi, Using Tophat v 2.0.11 for my paired-end data, I ran the default option of num allowed mismatches=2, but when going over my sam file and fetching the NM tags for each alignment, I see cases where...
Forum: Bioinformatics 02-05-2013, 10:24 AM
Replies: 13
Views: 31,573
Posted By vkartha
I try the same thing, but I don't get any...

I try the same thing, but I don't get any results:

library(biomaRt)
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
...
Forum: Bioinformatics 02-04-2013, 11:47 AM
Replies: 11
Views: 13,483
Posted By vkartha
I have a question, and I would really appreciate...

I have a question, and I would really appreciate it if I was to get a prompt reply!

I am performing an RNASeq analysis and I have paired-end 101 bp reads. I want to generate count data and perform...
Forum: Bioinformatics 12-04-2012, 09:19 AM
Replies: 2
Views: 3,712
Posted By vkartha
Hi, in an attempt to use Danpos using 2 bed tag...

Hi, in an attempt to use Danpos using 2 bed tag alignment files as input, I am unable to get it to work correctly, we get the following error:

python2.7 danpos.py tagAlign1-tagAlign2 -k 1
danpos...
Forum: Bioinformatics 11-20-2012, 08:06 AM
Replies: 28
Views: 14,309
Posted By vkartha
Collapsing identical reads

I understand how and why the collapsing has to be done, but I'm not sure what to use (even in terms of writing a simple script in python or R) to get the job done, given the files we're talking about...
Forum: RNA Sequencing 11-07-2012, 05:14 PM
Replies: 6
Views: 2,296
Posted By vkartha
Could any one point me to the best annotation...

Could any one point me to the best annotation file to count over annotated mature miRNA sequences? I am currently using the gff file off of mirbase (is this reliable?).
Forum: RNA Sequencing 07-10-2012, 05:28 PM
Replies: 22
Views: 24,608
Posted By vkartha
I ran Cufflinks with the -G flag (i.e. providing...

I ran Cufflinks with the -G flag (i.e. providing an annotation file (gtf file from UCSC) and suggesting to not perform novel transcript discovery) and I still got this XLOC id format. I am having...
Forum: Bioinformatics 07-05-2012, 04:06 AM
Replies: 16
Views: 5,611
Posted By vkartha
Hello, I am working with RNASEq data and we are...

Hello,
I am working with RNASEq data and we are to use 2 sets of 3 bam files each, i.e. 2 different conditions and 3 replicates per condition (which were obtained using Tophat2) with Cufflinks,...
Forum: Bioinformatics 07-03-2012, 09:06 PM
Replies: 0
Views: 1,778
Posted By vkartha
Cuffmerge error with gencode v12 gtf file

Hello,
I am working with RNASEq data and we are to use 2 sets of 3 bam files each, i.e. 2 different conditions and 3 replicates per condition (which were obtained using Tophat2) with...
Forum: Bioinformatics 06-07-2012, 06:18 AM
Replies: 11
Views: 22,516
Posted By vkartha
What do you mean by "weaker of the two pairs"?...

What do you mean by "weaker of the two pairs"? And if that is the case - how would I estimate what the right -r value to use would be, given it's so far off from what the actual estimated mean is?...
Forum: Bioinformatics 06-07-2012, 05:57 AM
Replies: 11
Views: 22,516
Posted By vkartha
assessing how -r affects Tophat output

Thanks for that Richard! Maybe you will be able to help me with my problem!

So to briefly outline what I did - I wanted to see how using different -r options for Tophat2 will affect my alignment...
Forum: Bioinformatics 06-07-2012, 05:18 AM
Replies: 11
Views: 22,516
Posted By vkartha
samtools flagstat dead?

I look now in the samtools manual and there is no longer a flagstat option to use for estimating these stats. Can anyone tell me why? I used it earlier to see how 'well' paired-end reads aligned to...
Forum: Bioinformatics 05-24-2012, 12:26 AM
Replies: 23
Views: 4,200
Posted By vkartha
So when I say best, I mean that I observed the...

So when I say best, I mean that I observed the highest % looking at the 'properly paired' flagstat output for +50.

I read that this 'properly paired' flag in the samtools flagstat output is a...
Forum: Bioinformatics 05-23-2012, 05:36 PM
Replies: 23
Views: 4,200
Posted By vkartha
Still unsure why I see +50 giving the best result

Can someone please address the issue I brought up here? How can the -r option that gives the best alignment results be way off? from the means I had estimated from the samples? In fact that option...
Forum: Bioinformatics 05-17-2012, 08:59 AM
Replies: 23
Views: 4,200
Posted By vkartha
So in terms of studying the effect of different...

So in terms of studying the effect of different -r options on aligning a given sample, I should look at the 'properly paired' statistic?

It is weird because I estimated the mean and std dev inner...
Forum: Bioinformatics 05-16-2012, 08:08 PM
Replies: 23
Views: 4,200
Posted By vkartha
I tried using samtools flagstat on one of the...

I tried using samtools flagstat on one of the output bam files and this is what I got :


43603331 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
43603331 + 0 mapped...
Forum: Bioinformatics 05-15-2012, 05:36 PM
Replies: 23
Views: 4,200
Posted By vkartha
-r option - Does it make a difference to the alignment?

Hey guys,
I have paired end reads on RNASeq data and I wanted to test run Tophat2 to map these reads for a given sample using 5 different -r values(that is the mean inner distance...
Forum: Bioinformatics 05-15-2012, 05:33 PM
Replies: 4
Views: 8,133
Posted By vkartha
Tophat2 -r option and alignment results

Hey guys,
I have paired end reads on RNASeq data and I wanted to test run Tophat2 to map these reads for a given sample using 5 different -r values(that is the mean inner distance...
Forum: Bioinformatics 04-18-2012, 07:45 AM
Replies: 0
Views: 909
Posted By vkartha
Tophat reads that weren't used for mapping?

Hey,
I was running TopHat for the first time for paired-end reads which were 101 bp long. Since it was a test run, I only performed it for the first 500,000 reads that were in each fastq file....
Forum: Bioinformatics 04-17-2012, 10:12 AM
Replies: 77
Views: 24,662
Posted By vkartha
I have data generated from Illumina Hiseq 2000...

I have data generated from Illumina Hiseq 2000 which uses 1:N and 2:N as opposed to /1 and /2 as suffices.
Ex:

@D8CXHXP1:222:C0HVHACXX:2:1101:1836:2165 2:N:0:ACAGTG

Do I just follow replacing...
Forum: RNA Sequencing 04-07-2012, 07:11 PM
Replies: 37
Views: 18,569
Posted By vkartha
transcriptome mapping

Hi Nicolas, I need to do this step, but I was wondering what the command for using 2 paired end read files (sample_R1.fastq and sample_R2.fastq) to map to a reference transcriptome would be?
How...
Showing results 1 to 25 of 28

 


All times are GMT -8. The time now is 02:21 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO