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Forum: Bioinformatics 06-22-2015, 02:04 PM
Replies: 6
Views: 3,252
Posted By id0
It looks like it performs an ABySS assembly. That...

It looks like it performs an ABySS assembly. That seems computationally intensive. More importantly, I am not sure how well it would do with dilute samples.
Forum: Bioinformatics 06-22-2015, 12:39 PM
Replies: 6
Views: 3,252
Posted By id0
Checking reads for contamination

Is there a tool to check for the source of contamination in sequencing reads? I am looking for something like BLAST, but that would summarize across many reads.

For example, I have a FASTQ that is...
Forum: Bioinformatics 04-13-2015, 08:34 AM
Replies: 2
Views: 3,269
Posted By id0
I am not sure why you are editing the chromosome...

I am not sure why you are editing the chromosome names or merging multiple files. iGenomes already comes with a combined genome FASTA file (Sequence/WholeGenomeFasta) that is already indexed.
Forum: Bioinformatics 04-09-2015, 07:59 AM
Replies: 9
Views: 2,316
Posted By id0
I used the Ensembl GFF. I also tried the NCBI...

I used the Ensembl GFF. I also tried the NCBI GFF. Similar result with both.

I use Picard CollectRnaSeqMetrics to collect the stats. It also generates graphs for normalized coverage across...
Forum: Bioinformatics 04-08-2015, 09:07 AM
Replies: 9
Views: 2,316
Posted By id0
The kit is ScriptSeq Complete Gold Kit...

The kit is ScriptSeq Complete Gold Kit (http://www.illumina.com/products/scriptseq-epidemiology.html). It even says on the website: "choose the FR=secondstrand option". That always works fine for me....
Forum: Bioinformatics 04-08-2015, 07:25 AM
Replies: 9
Views: 2,316
Posted By id0
I think you misunderstood my question. I am...

I think you misunderstood my question. I am familiar with the kit and I've used it for other species many times. The reads are always "reverse". Now I did bacteria and they are not "reverse".
Forum: Bioinformatics 04-07-2015, 01:23 PM
Replies: 9
Views: 2,316
Posted By id0
stranded bacterial RNA-seq

We did a stranded RNA-seq library prep on a bacterial sample (Mycobacterium tuberculosis). When using this kit for human/mouse/fly, the correct strand is always "second" or "reverse" strand...
Forum: Bioinformatics 04-07-2015, 01:14 PM
Replies: 5
Views: 8,254
Posted By id0
Most of the improvements are in the non-coding...

Most of the improvements are in the non-coding regions, so if you are doing exomes, you won't notice a difference.

My concern would be future-proofing. If these are your first exomes, you may as...
Forum: Bioinformatics 04-07-2015, 12:57 PM
Replies: 1
Views: 1,248
Posted By id0
The GTF file will only have exon boundaries. You...

The GTF file will only have exon boundaries. You need to generate the Wig or BigWig or TDF files from the BAM files. You can then input those into IGV.
Forum: Bioinformatics 01-08-2015, 12:21 PM
Replies: 6
Views: 1,876
Posted By id0
Thank you for that great explanation. The...

Thank you for that great explanation.

The only part I don't understand is this:

How would I provide that to the DESeq2 results function contrasts parameter?
Forum: Bioinformatics 01-08-2015, 11:53 AM
Replies: 6
Views: 1,876
Posted By id0
I didn't realize that the interaction and group...

I didn't realize that the interaction and group models would give the same results (at least with betaPrior=FALSE). That is really interesting.

So if I have two cell types (A and B) and two...
Forum: Bioinformatics 01-08-2015, 07:43 AM
Replies: 6
Views: 1,876
Posted By id0
DESeq2 multi-factor designs

In DESeq2, you can set up a multi-factor design like:
design(dds) <- formula(~ celltype + treatment)
This would give you the differences attributable to the "treatment" while accounting for the...
Forum: Bioinformatics 12-09-2014, 06:51 AM
Replies: 11
Views: 3,427
Posted By id0
storing raw sequences as BAMs versus FASTQs

Some sequencing facilities are storing the raw data as BAMs instead of FASTQs. Since it's faster and easier to generate FASTQs, there must be some benefit of converting to BAMs. I remember seeing...
Forum: Bioinformatics 09-29-2014, 09:53 AM
Replies: 1
Views: 1,192
Posted By id0
How to measure distribution of coverage across genome

Is there a good tool for evaluating distribution of reads across genome?

I realize there are several tools to calculate coverage in different ways, but then you usually with a large table that you...
Forum: Bioinformatics 08-25-2014, 10:57 AM
Replies: 7
Views: 3,093
Posted By id0
How would you use Cramer's V for heatmap? Do you...

How would you use Cramer's V for heatmap? Do you have any example?
Forum: Bioinformatics 08-05-2014, 02:52 PM
Replies: 13
Views: 4,960
Posted By id0
To give Qiime developers some credit, they are...

To give Qiime developers some credit, they are making progress in that regard. The latest version 1.8 added join_paired_ends.py and extract_barcodes.py scripts, which is a significant step forward.
Forum: Bioinformatics 07-25-2014, 02:48 PM
Replies: 9
Views: 2,870
Posted By id0
I wouldn't set -phred64, since Trimmomatic can...

I wouldn't set -phred64, since Trimmomatic can now detect quality automatically.

The fact that you are losing more than 90% of your reads for one of your libraries indicated that there is a...
Forum: Bioinformatics 07-25-2014, 11:19 AM
Replies: 2
Views: 3,240
Posted By id0
lncRNA target prediction

There are many tools for predicting miRNA targets. Does something like that exist for lncRNAs?
Forum: Bioinformatics 07-25-2014, 10:21 AM
Replies: 9
Views: 2,870
Posted By id0
I use Trimmomatic. It does both adapter and...

I use Trimmomatic. It does both adapter and quality trimming. The manual is very comprehensive, so you shouldn't really run into any questions.
Forum: Bioinformatics 07-24-2014, 10:32 AM
Replies: 12
Views: 3,664
Posted By id0
The cufflinks manual discusses the normalization...

The cufflinks manual discusses the normalization and dispersion estimation methods (all the way at the bottom at http://cufflinks.cbcb.umd.edu/manual.html). There are actually multiple options to...
Forum: Bioinformatics 07-24-2014, 10:27 AM
Replies: 9
Views: 2,870
Posted By id0
I fixed this by performing adapter and quality...

I fixed this by performing adapter and quality trimming before attempting assembly.
Forum: Bioinformatics 07-09-2014, 08:28 AM
Replies: 7
Views: 3,093
Posted By id0
Thanks for that suggestion. Switching the hclust...

Thanks for that suggestion. Switching the hclust method to ward had very noticeable results.

I guess my problem is really with the range of values. Most of the values end up in a small subset of...
Forum: Bioinformatics 07-08-2014, 12:41 PM
Replies: 7
Views: 3,093
Posted By id0
Improving heatmap plots

I sometimes make heatmaps for gene expression data. I proceed with the basic heatmap.2 method (based on DESeq recommendation):
heatmap.2( x, scale="row", trace="none",
dendrogram="both", Rowv=TRUE,...
Forum: Bioinformatics 07-01-2014, 09:41 AM
Replies: 3
Views: 1,096
Posted By id0
Cufflinks includes a special tool cuffmerge...

Cufflinks includes a special tool cuffmerge specifically for this purpose.
Forum: Bioinformatics 06-30-2014, 12:39 PM
Replies: 0
Views: 1,150
Posted By id0
TopHat --prefilter-multihits parameter

I am trying to understand TopHat's --prefilter-multihits parameter. According to the documentation:


I ran TopHat 1.4.1 (last version before 2) and 2.0.9 with just --GTF parameter on the same...
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