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Search: Posts Made By: Amative
Forum: Bioinformatics 12-12-2013, 11:53 AM
Replies: 0
Views: 2,338
Posted By Amative
GFF3 to GTF

Hi everyone:

I am using gff3_to_gtf_format.pl script from PASA to convert a gff3 formatted file to gtf. It keeps stopping at this message:
-indexing [augustus_masked-LG2-processed-gene-150.6] ...
Forum: Bioinformatics 09-25-2013, 08:37 AM
Replies: 0
Views: 1,564
Posted By Amative
gff statistics

Hello All,

I have got a GFF file back from maker. I need to calculate basic statistics for it, e.g. number of exons, average exon length, avg. intron length, avg. gene length, etc. Can anyone...
Forum: Bioinformatics 05-28-2013, 07:43 AM
Replies: 3
Views: 2,524
Posted By Amative
Any help, please!

Any help, please!
Forum: Bioinformatics 05-23-2013, 11:36 AM
Replies: 3
Views: 2,524
Posted By Amative
Clustering RNA-Seq RPKM/ReadsCount issues

Hello all,

I have an RNA-Seq expression data, both RPKM/ReadsCount. Number of records in each dataset is ~35,000 gene.

The samples are organised as follows:
Tissue #1: 5 stages , 2...
Forum: Bioinformatics 05-21-2013, 08:51 AM
Replies: 7
Views: 3,538
Posted By Amative
Hi Azazel, were you able to figure out you...

Hi Azazel, were you able to figure out you problem ?

Thanks!
Forum: Bioinformatics 04-28-2013, 05:01 PM
Replies: 3
Views: 17,315
Posted By Amative
Thanks a lot, I believe I got the idea :) The...

Thanks a lot, I believe I got the idea :)
The paper is super helpful
Forum: Bioinformatics 04-28-2013, 11:51 AM
Replies: 3
Views: 17,315
Posted By Amative
Batch effect

Hello everyone,

What is batch effect in rna-seq? How to check if one has it?
Any tools or links or documents would be great!

Thanks in advance
Forum: Bioinformatics 04-28-2013, 10:50 AM
Replies: 6
Views: 2,060
Posted By Amative
Excellent, Thanks Wally. I will definitely take...

Excellent, Thanks Wally.
I will definitely take a look at it, and hopefully I can do something similar.
Forum: Bioinformatics 04-26-2013, 12:15 PM
Replies: 6
Views: 2,060
Posted By Amative
Thanks a lot Wally :) Sounds interesting, and a...

Thanks a lot Wally :)
Sounds interesting, and a lot of work. I have never used any of the tools you suggested and excited to do so. Do you know of any links or documents and that list these steps...
Forum: Bioinformatics 04-22-2013, 06:48 PM
Replies: 6
Views: 2,060
Posted By Amative
Thanks Jimmy, I am not quite sure I understand...

Thanks Jimmy,
I am not quite sure I understand exactly how to do your second suggestion. Because I have already done the alignment to the genome and that is what caused my question.

Here is how...
Forum: Bioinformatics 04-22-2013, 09:40 AM
Replies: 6
Views: 2,060
Posted By Amative
Re-Annotate legacy gene predictions

Hello everyone,

I have a number of single-ended samples generated by Illumina-based Hsq2000. About 10 to 35 million 58-bp. A legacy annotation of an organism "genemark predictions". What are my...
Forum: Bioinformatics 04-08-2013, 12:21 PM
Replies: 5
Views: 1,640
Posted By Amative
Thanks GenoMax, for the suggestion I am working...

Thanks GenoMax, for the suggestion I am working on it.

I like the fastq_screen It saves some time!
Forum: Bioinformatics 04-03-2013, 10:05 AM
Replies: 6
Views: 3,463
Posted By Amative
Excellent, I will look at it as well

Excellent, I will look at it as well
Forum: Bioinformatics 04-03-2013, 08:11 AM
Replies: 5
Views: 1,640
Posted By Amative
Thanks swbarnes2 & rboettcher, @swbarnes2 ...

Thanks swbarnes2 & rboettcher,

@swbarnes2

I tried to blast the first ten reads from one of the samples I have, blast results were not that good. I tried to align against the available...
Forum: Bioinformatics 04-02-2013, 01:43 PM
Replies: 5
Views: 1,640
Posted By Amative
RNA-Seq alignment issue

Hello all,

I have been given paired-end RNA-Seq files to align against a couple of references. I used Bowtie2 to do the job. The alignment results were very low in most of the cases (less than 5%...
Forum: Bioinformatics 03-28-2013, 08:47 AM
Replies: 6
Views: 3,463
Posted By Amative
Thanks Daivd, That was helpful. I guess I am...

Thanks Daivd, That was helpful. I guess I am going to try Cufflinks and see how it goes. As I already have the SAM/BAM files, so it should be easy to try it.
Forum: Bioinformatics 03-25-2013, 08:09 AM
Replies: 6
Views: 3,463
Posted By Amative
Thanks David, I have been looking for tools to...

Thanks David, I have been looking for tools to analyze the output file from bowtie2 (SAM formatted) and found a couple (samtools flagstat and RSeQC):
The output from samtools flagstat is:

in...
Forum: Bioinformatics 03-24-2013, 09:06 AM
Replies: 6
Views: 3,463
Posted By Amative
RPKM for paired-end data

Hello,

I have aligned my RNA-Seq paired-end data to a reference using Bowtie2:
Bowtie2 -x Ref -1 pair1.fq -2 pair2.fq -S out.sam

In order to calculate RPKM we need to know the total number of...
Forum: Bioinformatics 02-12-2013, 03:14 PM
Replies: 9
Views: 2,500
Posted By Amative
Is there are any commercial web hosting places I...

Is there are any commercial web hosting places I can host my Gbrowse at ?

Thanks
Forum: Bioinformatics 02-12-2013, 03:07 PM
Replies: 9
Views: 2,500
Posted By Amative
@ girlwithglasses Any idea how much it's gonna...

@ girlwithglasses
Any idea how much it's gonna cost me to host the GMOD instance at Amazon cloud?
Forum: Bioinformatics 02-09-2013, 10:09 AM
Replies: 9
Views: 2,500
Posted By Amative
Thanks a lot :)

Thanks a lot :)
Forum: Bioinformatics 01-05-2013, 06:49 PM
Replies: 2
Views: 3,521
Posted By Amative
Thanks GenoMax, you are right, I was looking for...

Thanks GenoMax, you are right, I was looking for free stuff!
Although a couple of those listed at the link are for searching binding factors database NOT predicting. Please let me know if you come...
Forum: Bioinformatics 01-04-2013, 10:40 AM
Replies: 2
Views: 3,521
Posted By Amative
predict transcription factor binding sites in dna sequence

Hello all,

Can anyone here guide me to webtools or regular tools for predicting transcription factor binding sites in dna sequence. I know TESS (Transcription Element Search System) website. But...
Forum: Bioinformatics 12-19-2012, 04:32 PM
Replies: 1
Views: 1,316
Posted By Amative
Missing values in expression data matrix

Hello,

I have two expression data matrices (Reads Count and RPKM) both for the same set of samples. I have a lot of missing values in both. I am wondering if anyone can guide me to the correct way...
Forum: Bioinformatics 12-04-2012, 08:44 AM
Replies: 9
Views: 2,500
Posted By Amative
I ended up using Gbrowse, I took me forever to...

I ended up using Gbrowse, I took me forever to install it!! but finally I got it. But it seems there are many other alternatives. I have not tried any though.
Showing results 1 to 25 of 45

 


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