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Forum: Bioinformatics 09-28-2015, 08:46 AM
Replies: 3
Views: 1,024
Posted By sridharacharya
Thanks @GenoMax, could you quickly point me how...

Thanks @GenoMax, could you quickly point me how to start a new thread ? I could find buttons/links, to send replies, but not start a new thread.
Forum: Bioinformatics 09-28-2015, 08:11 AM
Replies: 3
Views: 1,024
Posted By sridharacharya
Lightbulb correlation in per base sequence quality profiles of multiplexed samples.

I have a question related to the "per base sequence quality" profiles.
In a Illumina HiSeq 150bp paired end runs of multiplexed samples, I found that the "per base mean sequence quality" profiles of...
Forum: Bioinformatics 09-28-2015, 07:47 AM
Replies: 366
Views: 201,132
Posted By sridharacharya
Thanks kmcarr!

Thanks kmcarr!
Forum: Bioinformatics 09-28-2015, 07:40 AM
Replies: 366
Views: 201,132
Posted By sridharacharya
Hi Simon, Is there a way in fastqc to turn...

Hi Simon,

Is there a way in fastqc to turn on reporting for every position rather than the default, 5 bp window for some analyses like the "Per base seqeunce quality"?

Thanks,
Sridhar
Forum: Bioinformatics 06-05-2014, 07:26 AM
Replies: 28
Views: 10,518
Posted By sridharacharya
I faced the same problem with plotMA of the...

I faced the same problem with plotMA of the DESeq2 package.
The command gives error
Error in as.vector(data):
no method for coercing this S4 class to a vector

I checked the input data to be of...
Forum: Bioinformatics 08-19-2011, 09:14 AM
Replies: 1
Views: 2,146
Posted By sridharacharya
perl pipeline for miRNA analysis

Hi,

I too have been searching for such a pipeline. So far, I could find only one resource, by Ryan D. Morin.
The URL is below.
http://www.bcgsc.ca/platform/bioinfo/software/novel-mirna-detection...
Forum: Illumina/Solexa 05-26-2011, 12:59 PM
Replies: 3
Views: 7,444
Posted By sridharacharya
Question single stranded DNA sequencing

I am curious about the same question as I am still not sure. Is it possible to use Illumina for sequencing single stranded DNA.
We are enriching some regions of genomic DNA by fragmentation,...
Forum: Bioinformatics 01-08-2011, 06:22 PM
Replies: 2
Views: 3,618
Posted By sridharacharya
Thanks frozenlyse. Clears my doubt!

Thanks frozenlyse. Clears my doubt!
Forum: Bioinformatics 01-07-2011, 03:15 PM
Replies: 2
Views: 3,618
Posted By sridharacharya
Post bowtie sam output, number of mismatches

Hi,

If I am right, bowtie options -n 0 -l 16 should not allow any mismatches in the seed region of 16. But the following result is puzzling me.

I am aligning sequencing reads using the above...
Forum: Bioinformatics 09-22-2010, 07:54 AM
Replies: 5
Views: 6,109
Posted By sridharacharya
The wrapper is indeed a good one to use...

The wrapper is indeed a good one to use compressed input files.
I tried to use it with SOLiD reads. Thanks for posting.
However, I found that, it can be useful only if the input is in fastq format....
Forum: RNA Sequencing 09-20-2010, 06:39 AM
Replies: 2
Views: 3,237
Posted By sridharacharya
Re: Regarding Unique reads, Unique alignments

malachig,

Thanks for the reply. I'll go through those discussions.

In my case, I am studying 3 types of experiments. I suppose the criteria to handle duplicate reads and handling of reads...
Forum: RNA Sequencing 09-17-2010, 08:41 AM
Replies: 2
Views: 3,237
Posted By sridharacharya
Regarding Unique reads, Unique alignments

I have few questions regarding the best practices that are adopted, in dealing with multiple alignments from a single read and presence of identical reads in the data (from Biology stand point for...
Forum: Bioinformatics 09-17-2010, 08:37 AM
Replies: 6
Views: 6,508
Posted By sridharacharya
Re: Aligning only unique reads in Bowtie

I have few questions regarding the best practices that are adopted, in dealing with multiple alignments from a single read and presence of identical reads in the data (from Biology stand point) :
...
Forum: RNA Sequencing 09-17-2010, 06:41 AM
Replies: 1
Views: 2,536
Posted By sridharacharya
Arrow Exon-Junction mapping: re-assigning CDS-mapped reads to chromosomes

Hi,

I am working with RNA-SEQ data and want to align SOLiD reads using publicly available software. Tophat cannot handle SOLiD reads, so I am going with Bowtie. But the problem is the mapping of...
Forum: RNA Sequencing 09-01-2010, 02:25 PM
Replies: 6
Views: 8,515
Posted By sridharacharya
Hi, I wanted to post a new thread, but cant...

Hi,

I wanted to post a new thread, but cant find "New Thread" button anywhere.

My question is :

Can Tophat handle csfasta files which are in color space format ? I think there is no command...
Forum: SOLiD 07-27-2010, 06:25 AM
Replies: 14
Views: 3,445
Posted By sridharacharya
Phillip, Thanks a lot for your suggestions,...

Phillip,

Thanks a lot for your suggestions, which have pointed the way to go for me. Yes, I have to discuss with my advisor and collaborators what the best action would be.

Thanks again. I...
Forum: SOLiD 07-26-2010, 08:04 AM
Replies: 14
Views: 3,445
Posted By sridharacharya
Hi Phillip, Thanks for your inputs. I could...

Hi Phillip,

Thanks for your inputs. I could run Corona-Lite matching pipeline on the csfasta file. Could you through some light on some of these aspects.

What is the difference between a bead...
Forum: SOLiD 07-19-2010, 10:59 AM
Replies: 14
Views: 3,445
Posted By sridharacharya
No idea, about the non-mapping reads. We have...

No idea, about the non-mapping reads. We have outsourced the analysis, so I don't have a clear idea about the details.

Do you know of any R/Bioconductor package for SOLiD data analysis. Basically...
Forum: SOLiD 07-19-2010, 08:01 AM
Replies: 14
Views: 3,445
Posted By sridharacharya
Yes, by 3491 starts, I was referring to the...

Yes, by 3491 starts, I was referring to the number of peaks. Yes the reference was same (human).
For the other runs (Input -genomic DNA control, the peaks look normal).
Forum: SOLiD 07-19-2010, 06:58 AM
Replies: 14
Views: 3,445
Posted By sridharacharya
Hi Phillip, There were, Number of...

Hi Phillip,

There were,

Number of reads: 15,277,642
Matched : 1,794,556 (11.72 %)

There were 3491 starts.

about 95% of the peaks were of length 51
Forum: SOLiD 07-18-2010, 09:13 PM
Replies: 14
Views: 3,445
Posted By sridharacharya
Hi Phillip, For both the steps, the method...

Hi Phillip,

For both the steps, the method used was shearing by sonication.

Specifically information for the second step (fragmenting of IPed DNA)

Sonication by, Covaris S2 System,...
Forum: SOLiD 07-15-2010, 02:17 PM
Replies: 14
Views: 3,445
Posted By sridharacharya
Hi Phillip, Thanks for the reply. It took...

Hi Phillip,

Thanks for the reply. It took some time to get the details.
---The size of the chromatin used for IP is about 300 to 500
---And the size of SOLiD fragment library created for...
Forum: SOLiD 07-13-2010, 07:31 AM
Replies: 14
Views: 3,445
Posted By sridharacharya
Exclamation question on SoLiD peak length

Hi,

I am new to analyzing SoLiD sequencing data. In our data, which is a ChIP-SEQ for histone modifications,
the maximum peak length detected was about 150bp and;
there were only about 18 peaks...
Forum: Site Feedback/Suggestions 05-26-2010, 12:50 PM
Replies: 3
Views: 3,884
Posted By sridharacharya
Smile Hi NGS Friends! ...

Hi NGS Friends!

http://seqanswers.com/forums/images/smilies/smile.gif Greeting to all!http://seqanswers.com/forums/images/smilies/smile.gif
I am Sridhar. Just joined the Community.
I am a PhD...
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