Forum: Bioinformatics
09-28-2015, 08:46 AM
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Replies: 3
Views: 1,028
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Forum: Bioinformatics
09-28-2015, 08:11 AM
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Replies: 3
Views: 1,028
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Forum: Bioinformatics
09-28-2015, 07:47 AM
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Replies: 366
Views: 202,272
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Forum: Bioinformatics
09-28-2015, 07:40 AM
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Replies: 366
Views: 202,272
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
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Forum: Bioinformatics
06-05-2014, 07:26 AM
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Replies: 28
Views: 10,650
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...
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Forum: Bioinformatics
08-19-2011, 09:14 AM
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Replies: 1
Views: 2,164
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...
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Forum: Illumina/Solexa
05-26-2011, 12:59 PM
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Replies: 3
Views: 7,467
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,...
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Forum: Bioinformatics
01-08-2011, 06:22 PM
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Replies: 2
Views: 3,639
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Forum: Bioinformatics
01-07-2011, 03:15 PM
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Replies: 2
Views: 3,639
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...
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Forum: Bioinformatics
09-22-2010, 07:54 AM
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Replies: 5
Views: 6,138
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....
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Forum: RNA Sequencing
09-20-2010, 06:39 AM
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Replies: 2
Views: 3,265
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...
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Forum: RNA Sequencing
09-17-2010, 08:41 AM
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Replies: 2
Views: 3,265
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...
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Forum: Bioinformatics
09-17-2010, 08:37 AM
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Replies: 6
Views: 6,589
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) :
...
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Forum: RNA Sequencing
09-17-2010, 06:41 AM
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Replies: 1
Views: 2,566
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Forum: RNA Sequencing
09-01-2010, 02:25 PM
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Replies: 6
Views: 8,550
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...
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Forum: SOLiD
07-27-2010, 06:25 AM
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Replies: 14
Views: 3,470
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...
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Forum: SOLiD
07-26-2010, 08:04 AM
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Replies: 14
Views: 3,470
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...
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Forum: SOLiD
07-19-2010, 10:59 AM
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Replies: 14
Views: 3,470
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...
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Forum: SOLiD
07-19-2010, 08:01 AM
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Replies: 14
Views: 3,470
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Forum: SOLiD
07-19-2010, 06:58 AM
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Replies: 14
Views: 3,470
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
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Forum: SOLiD
07-18-2010, 09:13 PM
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Replies: 14
Views: 3,470
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,...
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Forum: SOLiD
07-15-2010, 02:17 PM
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Replies: 14
Views: 3,470
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...
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Forum: SOLiD
07-13-2010, 07:31 AM
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Replies: 14
Views: 3,470
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...
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Forum: Site Feedback/Suggestions
05-26-2010, 12:50 PM
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Replies: 3
Views: 3,908
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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