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Forum: Illumina/Solexa 06-06-2012, 04:20 AM
Replies: 11
Views: 5,927
Posted By aparna
Hi Koadman, I had around 3million reads that...

Hi Koadman,

I had around 3million reads that were 3 prime contaminants and thats about it. As mentioned in my initial post, we have tried to look for Illumina/Epicenter adapters/ primers in our...
Forum: Illumina/Solexa 06-05-2012, 10:37 AM
Replies: 11
Views: 5,927
Posted By aparna
Hi Koadman and ECO , Thank you so much for your...

Hi Koadman and ECO ,
Thank you so much for your valuble insights and for the attachments.
I have not used MEME yet but looks like those 5 prime 14 bps are IS bias indeed.
I see the first 14 bp in...
Forum: Illumina/Solexa 06-04-2012, 01:03 PM
Replies: 11
Views: 5,927
Posted By aparna
Help with Nextera WGS data

Hi,

I am wondering if anyone here can provide me an answer to my question.

I am working on couple of WGS data - the libs are prepared using Illumina nextera and Truseq WG amplification kit ....
Forum: Bioinformatics 05-10-2012, 06:48 AM
Replies: 12
Views: 7,405
Posted By aparna
This is how it should look like: Sample ID ...

This is how it should look like:

Sample ID Bam File Notes
Y903GFAZ Y903GFAZ.bam Y903GFAZ

Aparna
Forum: RNA Sequencing 04-21-2012, 04:52 AM
Replies: 7
Views: 3,987
Posted By aparna
Hi, I suggest you read tophat paper for your...

Hi,
I suggest you read tophat paper for your questions.

WT mapping using bwa needs some sort of trimming in order to map good % of reads.Still you will miss splice reads and so many more,simply...
Forum: Bioinformatics 04-11-2012, 05:29 AM
Replies: 9
Views: 4,766
Posted By aparna
I would suspect at the library prep phase as...

I would suspect at the library prep phase as scooter.But since the data is out - I would try to improve mapping by using other aligners.
Bowtie is good for RNA seq with end to end mapping...
Forum: Bioinformatics 04-10-2012, 04:04 AM
Replies: 9
Views: 4,766
Posted By aparna
What %of reads were mapped?

What %of reads were mapped?
Forum: Bioinformatics 03-30-2012, 09:26 AM
Replies: 12
Views: 7,405
Posted By aparna
Hi Michael, Have you used RNAseQC? I am getting...

Hi Michael,
Have you used RNAseQC? I am getting an error - wondering if you know how to fix it.

Thanks,
Forum: Bioinformatics 03-29-2012, 11:06 AM
Replies: 7
Views: 3,586
Posted By aparna
Does anybody know how to fix this? Apparently I...

Does anybody know how to fix this? Apparently I emailed the developers - no response.
Forum: Bioinformatics 03-02-2011, 05:58 AM
Replies: 7
Views: 4,968
Posted By aparna
I worked on Newbler on transcriptome data,while...

I worked on Newbler on transcriptome data,while the concept of isotigs is good- 88k contigs with N50 951 is horrible.
With Illumina data I would advise you to look at Oasis/velvet and scripture.
Forum: Bioinformatics 02-28-2011, 05:51 AM
Replies: 8
Views: 5,452
Posted By aparna
Hey Alex, Thats all right. BLAST only...

Hey Alex,
Thats all right.

BLAST only outputs the extent that it matches to your sequences.If you want the entire sequneces from data base,the only way that I know to work around is to use -I T...
Forum: Bioinformatics 02-25-2011, 06:12 AM
Replies: 8
Views: 5,452
Posted By aparna
what do you mean by "I would like the output of...

what do you mean by "I would like the output of TblastN research"?
If I understand correctly,you are querying a nucleotide sequence againt nr with tblastn and would like to extract the...
Forum: Bioinformatics 02-24-2011, 10:18 AM
Replies: 89
Views: 65,847
Posted By aparna
Sorry I forgot to mention that I am trying to...

Sorry I forgot to mention that I am trying to perform alignment of indexed qseq files without
actually demultiplexing by supplying an empty formatted sample sheet (demultiplexing with pipeline sw is...
Forum: Bioinformatics 02-23-2011, 08:34 AM
Replies: 89
Views: 65,847
Posted By aparna
Thx.Thats refreshing. I have another question...

Thx.Thats refreshing.
I have another question to ask...about the qseq-mask. Right now I need to specify qseq-mask to get all 7 barcode basepairs reported in fastq files-yet If I want to do such...
Forum: Bioinformatics 02-23-2011, 05:57 AM
Replies: 89
Views: 65,847
Posted By aparna
Hi Seymon, Are you guys changing anything in...

Hi Seymon,

Are you guys changing anything in demultiplex process?Pretty confused to deal with the directories created during demultiplex process.
Thx.
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