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Forum: Bioinformatics 08-21-2020, 06:59 AM
Replies: 2
Views: 874
Posted By statsteam
Paired end seq read lengths are different

Hi all,

I recently acquired a dataset from GEO (HiSeq 2500, accession: GSE107029). It is a paired-end but the read_1 is 94 bp while read_2 is 100 bp. Since I've never seen paired-end data with...
Forum: Bioinformatics 05-28-2014, 05:45 PM
Replies: 1
Views: 1,185
Posted By statsteam
I figured out -a 6 parameter issue. It does not...

I figured out -a 6 parameter issue. It does not ensure individual read to have at least x bps on each side of junction. Instead, it ensures that each junction to have at least one read that meet the...
Forum: Bioinformatics 05-28-2014, 04:43 PM
Replies: 1
Views: 1,185
Posted By statsteam
tophat2 some parameters are not working (--no-novel-indels and -a)

I used tophat2 to map reads with --no-novel-indels and -a 6 parameters. Once the mapping is done, I examined the result (accepted_hits.bam) and found some lines with indels or some lines whose anchor...
Forum: RNA Sequencing 04-29-2014, 05:06 PM
Replies: 1
Views: 1,702
Posted By statsteam
As long as I know, MATS works with standard bam...

As long as I know, MATS works with standard bam files with NH:i:x attribute.
For me, all MATS run took about 24 hours. Hope this helps.
Forum: Bioinformatics 08-26-2013, 10:40 AM
Replies: 2
Views: 1,755
Posted By statsteam
Thanks a lot! By the way, it seems that SOAPfuse...

Thanks a lot! By the way, it seems that SOAPfuse requires paired-end reads while the reads I have is single-end. Any other tools for this purpose?
Forum: Bioinformatics 08-23-2013, 03:03 PM
Replies: 2
Views: 1,755
Posted By statsteam
gene fusion question

Dear all,

I am new to the gene fusion field and I would like to ask a basic question.

What is a good and easy program to use to detect gene fusion form RNA-Seq data?

Thank you in advance,...
Forum: RNA Sequencing 09-10-2012, 12:35 PM
Replies: 2
Views: 3,184
Posted By statsteam
The recent version of MATS (3.X.X) can handle...

The recent version of MATS (3.X.X) can handle replicates too. It is still in beta version tho.
Forum: Bioinformatics 02-01-2012, 01:23 PM
Replies: 5
Views: 4,330
Posted By statsteam
I agree that we'd better stick to cuffdiff for...

I agree that we'd better stick to cuffdiff for differentially expressed gene analysis. Doe cuffdiff have "paired"-analysis feature for the data with replicates? The paired-analysis feature is the...
Forum: Bioinformatics 02-01-2012, 12:09 PM
Replies: 5
Views: 4,330
Posted By statsteam
Cufflinks, differentially expressed genes

Hi,

I am trying to run edgeR or DEGseq using the output from cufflinks.
I usually use mapped reads count as an input to edgeR or DEGseq. What cufflinks output do I need to use for an input to...
Forum: Bioinformatics 11-19-2009, 08:12 AM
Replies: 1
Views: 2,512
Posted By statsteam
Running TopHat with 32bp or 36bp reads

Hi all,

I am trying to run TopHat with 32bp or 36bp reads. I am setting the length of segments to the half of the original length (16bp for 32bp reads and 18bp for 36bp reads). Besides it takes...
Forum: Bioinformatics 11-04-2009, 12:08 PM
Replies: 1
Views: 2,267
Posted By statsteam
TopHat questions

Hi,

I have a few general questions.

I am planning to do the junction mapping using 76bp reads.

What is the good anchor length to use (I am currently using 5 with a -5 option)?
Since the...
Forum: Bioinformatics 10-02-2009, 08:39 AM
Replies: 1
Views: 3,287
Posted By statsteam
Bowtie output

Hi all,

I got an RNA seq file that contains about 15million reads.
As it has more than 32bp reads, I decided to use Bowtie instead of my usual pick which is Eland.

So I mapped the sequence on...
Forum: Bioinformatics 09-17-2009, 01:53 PM
Replies: 3
Views: 7,939
Posted By statsteam
wiggle or bedGraph

Hi all,

I have about 300,000 lines of data I want to add to UCSC genome browser as a custom track.

Few lines of the data I have are:
=======
Chr Start End ...
Forum: RNA Sequencing 09-17-2009, 09:27 AM
Replies: 2
Views: 3,040
Posted By statsteam
I had the same problem before. What you need to...

I had the same problem before. What you need to do is to make your own bowtie index file using 'bowtie-build' command on fa files you downloaded from UCSC site.

Hope it helps,
Statsteam
Forum: Bioinformatics 09-15-2009, 09:36 AM
Replies: 7
Views: 6,039
Posted By statsteam
No, that is a data column because the output is...

No, that is a data column because the output is in bedGraph format.
When you copy and paste with correct chromosome name, it will draw a bedGraph based on the value of the data column.

In this...
Forum: Bioinformatics 09-15-2009, 08:20 AM
Replies: 7
Views: 6,039
Posted By statsteam
Thank you simon. I just started bowtie-build...

Thank you simon.
I just started bowtie-build with fasta files containing only chromosome names.

Statsteam
Forum: Bioinformatics 09-15-2009, 07:10 AM
Replies: 7
Views: 6,039
Posted By statsteam
Using TopHat output files with UCSC genome browser

Hi all,

Recently, I ran TopHat with 76bp reads data and got the results (sam, bed, and wig files).

Actual a few lines of my input (fasta file) are:
>HWUSI-EAS366:4:1:4:624#0/1:...
Forum: RNA Sequencing 09-14-2009, 02:38 PM
Replies: 2
Views: 2,734
Posted By statsteam
Using tophat results via UCSC genome browser

Hi all,

Recently, I ran TopHat with 76bp reads data and got the results (sam, bed, and wig files).

Actual a few lines of my input (fasta file) are:
>HWUSI-EAS366:4:1:4:624#0/1:...
Forum: Bioinformatics 09-09-2009, 12:06 PM
Replies: 1
Views: 2,723
Posted By statsteam
TopHat questions (indexes and seq length)

Hi all,

I just downloaded and installed tophat with bowtie.

Using the test_data, it worked fine and found some junctions.

I went ahead and ran Chris Burge's cerebellum data (12M reads, 36bp)...
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