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Forum: RNA Sequencing 02-13-2014, 06:13 AM
Replies: 23
Views: 18,618
Posted By pbluescript
RSeQC can do this. http://rseqc.sourceforge.net/

RSeQC can do this.
http://rseqc.sourceforge.net/
Forum: Bioinformatics 08-07-2013, 06:31 PM
Replies: 11
Views: 10,955
Posted By pbluescript
If you got that error, then one of the files you...

If you got that error, then one of the files you used originally is either missing data or has data with names that do not match.

To get this information from your GTF files, you could use the...
Forum: Bioinformatics 08-07-2013, 06:30 AM
Replies: 11
Views: 10,955
Posted By pbluescript
Your GTF and FASTA files do not have the same...

Your GTF and FASTA files do not have the same reference sequences. The issue is likely from combining Ensembl and UCSC. For example, in Ensembl, chromosome X is referred to as "X" while in UCSC, it...
Forum: Bioinformatics 06-13-2013, 05:45 AM
Replies: 11
Views: 10,955
Posted By pbluescript
You have to get a gtf file that matches the...

You have to get a gtf file that matches the genome you aligned to. For example, UCSC designates chromosome 1 as "chr1" and Ensembl designates it as "1". If they do not match, most programs will throw...
Forum: Academic/Non-Profit Jobs 06-13-2013, 05:38 AM
Replies: 0
Views: 824
Posted By pbluescript
SENIOR BIOINFORMATICS SPECALIST - Tufts Technology Services

https://2xrecruit.kenexa.com/kr/cc/jsp/public/EmailJobDetail.jsf?npi=665B137F6797C0F7213DE82547E92B47&rand=188E0ACBD8EBF9AF5D9E079586D398451F95986920B23B8A67761D8D86561457

Reporting directly to...
Forum: Sample Prep / Library Generation 05-13-2013, 05:44 AM
Replies: 1
Views: 2,072
Posted By pbluescript
Yes. They work fine.

Yes. They work fine.
Forum: Bioinformatics 05-10-2013, 05:09 AM
Replies: 11
Views: 3,997
Posted By pbluescript
Haha... that's what I get for reading your posts...

Haha... that's what I get for reading your posts too quickly. Something is a bit odd about your flag fields. I've never had this particular problem before.

What happens if you use samtools view -f...
Forum: Bioinformatics 05-10-2013, 05:01 AM
Replies: 11
Views: 3,997
Posted By pbluescript
BWA outputs mapped as well as unmapped reads to...

BWA outputs mapped as well as unmapped reads to the SAM file.
Forum: Bioinformatics 05-10-2013, 04:51 AM
Replies: 11
Views: 3,997
Posted By pbluescript
You are getting those results because BWA only...

You are getting those results because BWA only gave you unique alignments.
Forum: Bioinformatics 05-10-2013, 04:00 AM
Replies: 11
Views: 3,997
Posted By pbluescript
How do you know it's not working? If you get 0...

How do you know it's not working? If you get 0 from this command, it is working.

samtools view -f 256 your_file.bam | wc -l

BWA can do soft clipping while the original Bowtie does not. Maybe...
Forum: Bioinformatics 05-10-2013, 03:38 AM
Replies: 11
Views: 3,997
Posted By pbluescript
There are many ways to do this. Here's one you...

There are many ways to do this. Here's one you can use if you have a BAM file of reads aligned with BWA.

samtools view -F 256 your_file.bam | wc -l

This will remove all the reads that are not...
Forum: Core Facilities 05-02-2013, 05:42 PM
Replies: 3
Views: 2,833
Posted By pbluescript
It is just another variable added to the...

It is just another variable added to the experiment that you will have to properly control for. I would recommend not doing it unless you had some sort of spike in control that you could use to...
Forum: Bioinformatics 04-24-2013, 10:06 AM
Replies: 3
Views: 3,424
Posted By pbluescript
Cufflinks FPKM_conf_hi smaller than FPKM

I am running into an issue with the current version of Cufflinks (2.1.1) that I have not seen in previous versions. Some of the FPKM_conf_hi values are smaller than the FPKM values. Since the...
Forum: RNA Sequencing 03-18-2013, 05:48 AM
Replies: 1
Views: 1,188
Posted By pbluescript
You should go with a method designed to correct...

You should go with a method designed to correct for multiple testing. Something like Cufflinks, DESeq, rsem, etc. will probably do a better job than a single test.
Forum: Illumina/Solexa 03-13-2013, 07:19 AM
Replies: 76
Views: 40,596
Posted By pbluescript
The 100 bp ladder in the image is this one: ...

The 100 bp ladder in the image is this one:
http://products.invitrogen.com/ivgn/product/15628019
The 1kb+ ladder in the image is this one:
http://products.invitrogen.com/ivgn/product/10787026
Forum: Bioinformatics 03-09-2013, 06:45 AM
Replies: 3
Views: 1,591
Posted By pbluescript
This software can do many of the things you want:...

This software can do many of the things you want:
https://code.google.com/p/rseqc/

If you want to get really specific about the types of RNA that are represented in your sample, then using...
Forum: Bioinformatics 03-04-2013, 04:09 AM
Replies: 2
Views: 2,636
Posted By pbluescript
From the Cufflinks manual: --max-bundle-frags...

From the Cufflinks manual:
--max-bundle-frags <int> Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are marked with status HIDATA. Default: 1000000

Just...
Forum: RNA Sequencing 02-14-2013, 03:49 AM
Replies: 1
Views: 3,039
Posted By pbluescript
Tophat can sometimes have trouble mapping reads...

Tophat can sometimes have trouble mapping reads with a lot of low quality bases on the end. Trimming the reads might help with that, but shorter reads are more likely to map to multiple locations. If...
Forum: RNA Sequencing 01-17-2013, 01:03 PM
Replies: 9
Views: 5,816
Posted By pbluescript
Since you have shorter reads, you might need to...

Since you have shorter reads, you might need to set --segment-length and --min-anchor-length lower.

You could also try STAR. It finds spliced alignments by looking for the largest portion of a...
Forum: RNA Sequencing 01-10-2013, 11:21 AM
Replies: 9
Views: 5,816
Posted By pbluescript
You can use something like Trimmomatic to trim...

You can use something like Trimmomatic to trim off the adapter sequences first.
Forum: Sample Prep / Library Generation 01-03-2013, 01:26 PM
Replies: 9
Views: 7,217
Posted By pbluescript
Does your ladder already have a loading dye added...

Does your ladder already have a loading dye added to it or do you add it after the size selection?
Forum: RNA Sequencing 12-11-2012, 03:32 AM
Replies: 7
Views: 2,484
Posted By pbluescript
Like pmiguel said, that comment doesn't make...

Like pmiguel said, that comment doesn't make sense.
Where stranded hasn't caught up is in dealing with small amounts of RNA or highly fragmented samples. Some of my samples simply can't be done with...
Forum: Bioinformatics 12-05-2012, 04:35 AM
Replies: 4
Views: 2,712
Posted By pbluescript
You can do it using piping. intersectBed -a...

You can do it using piping.

intersectBed -a 1.bed -b 2.bed | intersectBed -a stdin -b 3.bed | ... and so on.
Forum: Bioinformatics 12-04-2012, 11:28 AM
Replies: 14
Views: 6,027
Posted By pbluescript
Might be a good way to QC the survey. :)

Might be a good way to QC the survey. :)
Forum: Bioinformatics 11-20-2012, 04:07 AM
Replies: 24
Views: 15,234
Posted By pbluescript
The UCSC gene name substitution is a problem I've...

The UCSC gene name substitution is a problem I've run into before too.
Here's a blog post I found that offers a solution for anyone who's interested:...
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