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Forum: Bioinformatics 10-04-2016, 11:54 AM
Replies: 0
Views: 856
Posted By mattanswers
gene overlaps in Arabidopsis GFF file

Has anyone ever looked at a GFF to find all the genes that have base overlaps ?
These genes can be counted a 0 in HTSeq and Arabidopsis is a dense genome, so I was wondering if anyone has done this...
Forum: Bioinformatics 12-08-2015, 01:42 PM
Replies: 4
Views: 991
Posted By mattanswers
Go to Biostars, as suggested above, and then...

Go to Biostars, as suggested above, and then click on Planethttps://www.biostars.org/planet/. A place to start with regard to blogs.
Forum: Bioinformatics 10-16-2015, 03:55 PM
Replies: 1
Views: 786
Posted By mattanswers
mapped reads distributed over genome features

I am not quite sure as to what you mean when you say 'the mark she wants me to analyze'.

Was the ChIP-Seq experiment done with antibodies to KAP-1 or Pol II ?

If this is the case, then...
Forum: Illumina/Solexa 03-17-2015, 01:01 PM
Replies: 1
Views: 1,099
Posted By mattanswers
You can check MGH,...

You can check MGH, https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/crispr_sequencing_main.jsp
Forum: RNA Sequencing 02-17-2015, 01:17 PM
Replies: 0
Views: 560
Posted By mattanswers
Cuffdiff dilemma

I have 4 samples, each in triplicate (A1, A2, A3; B1, B2, B3; C1, C2, C3; D1, D2, D3)

When I use Cuffdiff to compare within each sample, say A1 to A2 or B2 to B3, I get DE genes and...
Forum: Bioinformatics 01-22-2015, 12:15 PM
Replies: 7
Views: 1,611
Posted By mattanswers
OK. Thank you for clarifying that. (And also...

OK. Thank you for clarifying that.
(And also for making DESeq2 !)
Forum: Bioinformatics 01-22-2015, 12:06 PM
Replies: 7
Views: 1,611
Posted By mattanswers
Thank you very much for your answers Dario, Devon...

Thank you very much for your answers Dario, Devon and Michael !
Forum: Bioinformatics 01-21-2015, 08:08 PM
Replies: 7
Views: 1,611
Posted By mattanswers
We have wild type condition A and wild type...

We have wild type condition A and wild type condition B as well as treated condition A and treated condition B. So, we would like to see changes in gene expression between condition A and condition...
Forum: Bioinformatics 01-21-2015, 07:17 PM
Replies: 2
Views: 1,074
Posted By mattanswers
supervised clustering

I would suggest supervised clustering. You can input a given gene's expression pattern and the rest of the genes will be clustered by what genes show the most similar patterns.

Class Neighbors...
Forum: Bioinformatics 01-21-2015, 04:39 PM
Replies: 7
Views: 1,611
Posted By mattanswers
4 conditions in DESeq2

I have four conditions A, B, C, and D that each have three HTSeq count files.

I want to use DESeq2 to compare A to B, A to C, A to D, B to C, B to D etc.

With DESeq, I would bring all the 12...
Forum: Bioinformatics 07-11-2014, 03:40 PM
Replies: 2
Views: 2,533
Posted By mattanswers
Thanks. I had the same problem again, and I just...

Thanks. I had the same problem again, and I just re-ran the cuffmerge command in the cuffmerge output folder it had created in the first try.
Forum: Bioinformatics 01-08-2014, 03:56 PM
Replies: 13
Views: 2,468
Posted By mattanswers
Arabidopsis

Will it include Arabidopsis data ?
Forum: Bioinformatics 08-14-2013, 12:20 PM
Replies: 4
Views: 2,489
Posted By mattanswers
Thanks again for your help, GenoMax. My...

Thanks again for your help, GenoMax.

My sequence length is only 50 bases and the quality is very good.

From what I read on the linked site, it seems that I have 6 kmers that are 50-fold...
Forum: Bioinformatics 08-13-2013, 01:18 PM
Replies: 4
Views: 2,489
Posted By mattanswers
Thank you very much, GenoMax, for the links. They...

Thank you very much, GenoMax, for the links. They are very informative.

This is RNA-Seq. It seems the first 12 or so bases are due to 'random' priming, but I was also wondering about why the...
Forum: Bioinformatics 08-13-2013, 11:26 AM
Replies: 4
Views: 2,489
Posted By mattanswers
fastqc kmer relative enrichment

I was wondering how to interpret the Kmer content graph in fastqc. I have attached it. It seems from my graph that 50% of all reads have the 6 kmers listed ? Is this a normal graph ?
Forum: Bioinformatics 02-04-2013, 02:47 PM
Replies: 2
Views: 2,533
Posted By mattanswers
error in Cufflinks v2.0.2 when using Cuffmerge

When I run Cuffmerge, I receive the following error:
You are using Cufflinks v2.0.2, which is the most recent release.
Error creating output file tmp_meta_asm.stats!
[FAILED]
Error: could...
Forum: Bioinformatics 01-30-2013, 11:25 AM
Replies: 13
Views: 14,731
Posted By mattanswers
Thank you for your help, and also for writing and...

Thank you for your help, and also for writing and sharing FastaHack.
Forum: Bioinformatics 01-29-2013, 04:02 PM
Replies: 13
Views: 14,731
Posted By mattanswers
Thank you ekg for your fastahack tool. The tool...

Thank you ekg for your fastahack tool. The tool seems to extract the sequence by its position in the fasta file. I was wondering if it can extract a provided subsequence from the fasta file, and if...
Forum: Bioinformatics 01-25-2013, 11:55 AM
Replies: 1
Views: 730
Posted By mattanswers
Some info to clarify the above question

Let me add, that I realize the difficulties of 'significant' genes when you do not have duplicates.

The purpose of my analysis is to get an idea of the consistency of results between the two...
Forum: Bioinformatics 01-25-2013, 11:50 AM
Replies: 1
Views: 730
Posted By mattanswers
Cuffdiff output seems inconsistant

(I am transferring this question from the RNA-Seq Forum (where I have deleted it) to this Forum)

I have two sets of time series data. Same conditions, just done on different days. With each...
Forum: RNA Sequencing 01-23-2013, 04:57 PM
Replies: 0
Views: 865
Posted By mattanswers
Cuffdiff output seems inconsistant

I think this question is better suited to the Bioinformatics Forum, so I have moved it there.
Forum: Bioinformatics 01-18-2013, 02:29 PM
Replies: 17
Views: 1,951
Posted By mattanswers
I have used LTP Viewer, if you want to quickly...

I have used LTP Viewer, if you want to quickly view a large file as well as search within it, but not much as an editor.

http://www.swiftgear.com/ltfviewer/features.html
Forum: Bioinformatics 10-25-2012, 04:35 PM
Replies: 0
Views: 1,555
Posted By mattanswers
TopHat did not find any junctions in GTF file

I can not figure out why I am getting the message, 'TopHat did not find any junctions in GTF file',
as well as the error, 'Couldn't build bowtie index with err = 1'.

When this file,...
Forum: Bioinformatics 02-08-2012, 12:13 PM
Replies: 2
Views: 2,151
Posted By mattanswers
You can see if DeconSeq will help: ...

You can see if DeconSeq will help:
http://deconseq.sourceforge.net/
Forum: Bioinformatics 02-02-2012, 02:32 PM
Replies: 20
Views: 11,544
Posted By mattanswers
Looking at the positions of the sequences, I...

Looking at the positions of the sequences, I would see if the sequences: CAGCACCAGCA or CAGCACCACC are part of your primers.
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