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Forum: Bioinformatics 01-11-2011, 04:45 AM
Replies: 0
Views: 1,549
Posted By agc
Cuffdiff outputs mostly FAIL

Hi,

I used TopHat on two short-read SOLiD samples, then cufflinks with refFlat as my GTF, then cuffcompare to find differences between the samples. I'm looking for splicing differences, however in...
Forum: Bioinformatics 01-10-2011, 03:13 AM
Replies: 11
Views: 8,283
Posted By agc
How long should paired-end alignment run?

I'm aligning Illumina paired-end reads using bwa for the first time. With short reads from the same sample (yeast) alignment took 2-3 hours, but now I've been waiting for results for 4 days. It seems...
Forum: Bioinformatics 01-05-2011, 04:34 AM
Replies: 2
Views: 1,621
Posted By agc
Ended up writing a short python script that does...

Ended up writing a short python script that does this, although I also found FASTX:
http://hannonlab.cshl.edu/fastx_toolkit/download.html
Forum: Bioinformatics 01-04-2011, 03:44 AM
Replies: 2
Views: 1,621
Posted By agc
Extracting reads with specific barcodes

Hi,

I've received Illumina PE files, which I've been told contain several samples, and that the barcode I want is GT. From what I've understood, barcodes are a sequence of 2-3 bases added to the...
Forum: Bioinformatics 12-27-2010, 01:22 AM
Replies: 35
Views: 10,396
Posted By agc
I'm using TopHat version 1.1.4 with bowtie...

I'm using TopHat version 1.1.4 with bowtie version 0.12.7.0, and getting the following error with two out of four samples:
File "~/Tools/TopHat/tophat-1.1.4.Linux_x86_64/tophat", line 1520, in...
Forum: RNA Sequencing 12-20-2010, 12:52 AM
Replies: 2
Views: 2,476
Posted By agc
Gapped alignment with RNA-Seq

It seems that the mainstream tools used for RNA-Seq analysis are Tophat and Cufflinks. However, since Tophat is bowtie-based it can't do gapped alignment with short reads. I thought of mapping with...
Forum: Bioinformatics 11-24-2010, 03:47 AM
Replies: 1
Views: 3,286
Posted By agc
mpileup on haploid samples

Hi,

When running `samtools mpileup` with no parameters , it says that mpileup assumes diploid individuals. I'm working with haploid samples - does that mean I have to find a different SNP / Indel...
Forum: Bioinformatics 11-21-2010, 11:07 PM
Replies: 1
Views: 3,215
Posted By agc
Max Mapping / SNP / Consensus Quality in pileup files

I'm having trouble finding documentation on these values - does anyone know how they are calculated, or what they mean?

Thanks.
Forum: Bioinformatics 11-21-2010, 05:06 AM
Replies: 1
Views: 1,722
Posted By agc
Tablet not showing pileup indels

Hi,

I have a pileup file with the following line:
chr4 103518793 * */+TA 20 20 33 6 * +TA 5 1 0 0 0

I understand this implies that there is an indel at position 103518793 on chr4. However,...
Forum: Bioinformatics 11-18-2010, 03:34 AM
Replies: 3
Views: 2,078
Posted By agc
Thanks a lot! It seems to be working. Any idea...

Thanks a lot! It seems to be working. Any idea why these files are in this format? They're supposed to be illumina files.
Forum: Bioinformatics 11-17-2010, 04:17 AM
Replies: 3
Views: 2,078
Posted By agc
unrecognized .txt format

Hi,

I recently received data from illumina, and I am unable to determine the file format or how to convert it to a fastq for bwa. I found lots of documentation on a format called qseq, and several...
Forum: SOLiD 10-25-2010, 01:20 AM
Replies: 5
Views: 4,494
Posted By agc
A new version of SHRiMP was released just last...

A new version of SHRiMP was released just last month, so it can't be that outdated. And I think I saw somewhere that it does take quality values into consideration.
Forum: SOLiD 10-19-2010, 12:52 AM
Replies: 5
Views: 4,494
Posted By agc
SHRiMP and SOLiD Qualities

I want to run SHRiMP on SOLiD data, but despite reading the manual I can't find a parameter that allows me to give the .qual file as input. Does SHRiMP not consider quality values at all?
Forum: Bioinformatics 07-22-2010, 04:18 AM
Replies: 3
Views: 2,489
Posted By agc
Thanks for the quick reply! 1) Genome...

Thanks for the quick reply!

1) Genome re-sequencing
2) Single ~50bp reads
3) Not sure where I can obtain that information.
4) S. Cerevisiae

The translocation occurred within the same...
Forum: Bioinformatics 07-22-2010, 01:24 AM
Replies: 3
Views: 2,489
Posted By agc
Using 50bp short-reads to find a translocation

I know of a translocation that occurred (I also know the sequence that was translocated) in my sequenced DNA, but I'm not sure where it was translocated to, and the reads of the translocated sequence...
Forum: Bioinformatics 07-01-2010, 06:14 AM
Replies: 8
Views: 5,538
Posted By agc
I apologize for bumping this, but if there is no...

I apologize for bumping this, but if there is no such program, we will attempt to write our own, but if there is already a software option for this, we'd rather utilize it then put in the time and...
Forum: Bioinformatics 06-27-2010, 06:55 AM
Replies: 8
Views: 5,538
Posted By agc
Utilizing a reference sample, is there a program...

Utilizing a reference sample, is there a program (or samtools command) that can output the coordinates and sequences on the reference sequence where there is no coverage by the reads? We can roughly...
Forum: Bioinformatics 06-22-2010, 04:02 AM
Replies: 8
Views: 5,538
Posted By agc
Our data is not mate-pair (50bp fragment...

Our data is not mate-pair (50bp fragment library), but I would like to find fairly large indels (>200bp). Is this possible? I've read up on gapped aligners (BFAST and BWA), but they seem to be...
Forum: Bioinformatics 06-20-2010, 04:32 AM
Replies: 8
Views: 5,538
Posted By agc
Using samtools/tablet to find indels

As I understand, the following code should extract indels from a bam file and output them in pileup format:
samtools pileup -if <ref.fa> <file.sorted.bam>

This command outputs nothing, however,...
Forum: Bioinformatics 06-20-2010, 02:09 AM
Replies: 366
Views: 179,544
Posted By agc
I'd like to run FastQC on SOLiD reads. I saw that...

I'd like to run FastQC on SOLiD reads. I saw that someone did this using solid2fastq. Is it possible to do it without running solid2fastq? IE, would it work with only the SOLiD 'quals' file?

EDIT:...
Forum: Bioinformatics 06-19-2010, 11:34 PM
Replies: 123
Views: 41,536
Posted By agc
Yes, there was a problem with the BAM file -...

Yes, there was a problem with the BAM file - several sequence names were left blank (due to my reference fasta file including a space between the '>' sign and the sequence name - IE '> chr07' instead...
Forum: Bioinformatics 06-17-2010, 05:41 AM
Replies: 4
Views: 2,644
Posted By agc
Quality Control and Quality Values

As I understand it, each base in a read is given a quality value, and the higher the value the more likely the base read is accurate. I don't understand some things about the QV though -

1) How...
Forum: Bioinformatics 06-07-2010, 02:48 AM
Replies: 3
Views: 7,638
Posted By agc
What if it is more than one base that is missing,...

What if it is more than one base that is missing, IE:

read: ATGAT----ATGA
ref: ATGATGATGATGA

Will that be aligned as well? What is the maximum of missing bases allowed for it to still be...
Forum: Bioinformatics 06-07-2010, 02:43 AM
Replies: 123
Views: 41,536
Posted By agc
SAMSequenceDictionary

Hi,

While attempting to view a sorted BAM file (that has been indexed) with a fasta reference on Tablet, I receive the following error:

java.lang.IllegalArgumentException: Cannot add sequence...
Forum: Bioinformatics 05-20-2010, 06:01 AM
Replies: 3
Views: 7,638
Posted By agc
Gapped Alignment

Several short-read aligners claim that they can perform gapped alignment - I'm new to short-read aligners, and I don't understand what 'gapped alignment' means. How is it different from standard...
Showing results 1 to 25 of 26

 


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