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Forum: Bioinformatics 10-27-2010, 02:46 AM
Replies: 11
Views: 15,140
Posted By Bio.X2Y
Hi, Below is an example (both ends shown). ...

Hi,
Below is an example (both ends shown).

I'm not sure what you mean by this being an artefact of SW alignment? I would have thought that trimming would either (a) be allowed or (b) not allowed....
Forum: Bioinformatics 10-27-2010, 02:08 AM
Replies: 11
Views: 15,140
Posted By Bio.X2Y
Hi, I didn't specify a "q" value, and the BWA...

Hi, I didn't specify a "q" value, and the BWA manual implies that this means a default value of "0" is used.

The official description of "q" is a bit cryptic for a non-mathematician, but I thought...
Forum: Bioinformatics 10-26-2010, 09:57 AM
Replies: 11
Views: 15,140
Posted By Bio.X2Y
BWA Soft Clipping

Hi,

When I run BWA without specifying a "q" value (which defaults to 0 as I understand it from the manual), I would not expect any trimming to occur.

However, the resulting alignments have lots...
Forum: Illumina/Solexa 10-16-2010, 12:42 PM
Replies: 9
Views: 6,500
Posted By Bio.X2Y
Hi Simon, thanks for this. Out of interest, when...

Hi Simon, thanks for this. Out of interest, when you say you do 10% of a lane, how is this done? I'm not very familiar with the sequencing procedure itself, but I imagined it was an all-or-nothing,...
Forum: Illumina/Solexa 10-12-2010, 12:20 PM
Replies: 9
Views: 6,500
Posted By Bio.X2Y
Hi, is it possible to get unpaired reads from a...

Hi, is it possible to get unpaired reads from a paired-end experiment? I'm not very familiar with the procedure.
Forum: Illumina/Solexa 10-12-2010, 07:22 AM
Replies: 9
Views: 6,500
Posted By Bio.X2Y
Thanks Pepe, that makes sense. Does anyone...

Thanks Pepe, that makes sense.

Does anyone else have other possible explanations? Cheers
Forum: Illumina/Solexa 10-08-2010, 12:37 PM
Replies: 9
Views: 6,500
Posted By Bio.X2Y
Why are Illumina paired-end SRA datasets made up of 3 FASTQ files?

I'm looking at some NCBI SRA datasets for Paired-End Illumina Rna-seq.

In each case, the dataset is made up of 3 fastq files, even though I would only expect 2 (one for each end).

Example:
...
Forum: Bioinformatics 07-08-2010, 10:28 AM
Replies: 3
Views: 1,935
Posted By Bio.X2Y
I'm not aware of anything convenient for doing...

I'm not aware of anything convenient for doing this, but someone else might be able to shed light.

If you are comfortable with programming, I'd sort the file by name, leaving the header records on...
Forum: Bioinformatics 07-04-2010, 10:55 AM
Replies: 5
Views: 2,824
Posted By Bio.X2Y
I can see nothing wrong with the format after a...

I can see nothing wrong with the format after a quick look; perhaps you could try e-mailing Cole, he might be able to shed light on whether the format is the issue.
Forum: Bioinformatics 07-04-2010, 10:19 AM
Replies: 5
Views: 2,824
Posted By Bio.X2Y
I'm not sure where you got your GFF3, but some...

I'm not sure where you got your GFF3, but some others have had issues taking UCSC GTF files and converting them to GFF3 files that TopHat can use. As you probably know, TopHat can also have a list of...
Forum: Bioinformatics 07-04-2010, 10:09 AM
Replies: 5
Views: 2,824
Posted By Bio.X2Y
Actually, sorry, didn't notice you were referring...

Actually, sorry, didn't notice you were referring to an index there ; ignore my comments!
Forum: Bioinformatics 07-04-2010, 10:06 AM
Replies: 5
Views: 2,824
Posted By Bio.X2Y
There's a space character in your file location...

There's a space character in your file location on your command line ("genomic reads") - perhaps that's why tophat is reporting "Empty input file". Try renaming that directory and trying again.
Forum: Bioinformatics 06-29-2010, 06:05 AM
Replies: 3
Views: 2,098
Posted By Bio.X2Y
Thanks epigen, I guess it's an optional way of...

Thanks epigen, I guess it's an optional way of using the format then.
Forum: Bioinformatics 06-28-2010, 09:38 AM
Replies: 3
Views: 2,098
Posted By Bio.X2Y
SAM Format - SEQ field '='

Hi,

I was just looking through the SAM format spec again and I've come across something that confuses me.

The text for the 'SEQ' field is:
"query SEQuence; = for a match to the reference;...
Forum: Bioinformatics 06-16-2010, 07:24 AM
Replies: 2
Views: 2,763
Posted By Bio.X2Y
I've raised this question on the Bowtie...

I've raised this question on the Bowtie sourceforge (I can't find a place to raise CuffLinks specific questions/bugs):...
Forum: Bioinformatics 06-16-2010, 02:57 AM
Replies: 2
Views: 1,932
Posted By Bio.X2Y
As far as I know you don't create a subdirectory...

As far as I know you don't create a subdirectory for each index. just place the 6 hg18 files in the indexes directory.
Forum: Bioinformatics 06-15-2010, 05:32 AM
Replies: 4
Views: 5,229
Posted By Bio.X2Y
Hi snp_analyser. I'm afraid there is no good...

Hi snp_analyser. I'm afraid there is no good value - the inner distances depend on the sizes of your fragments and the lengths of your reads, which are experiment specific.

We typically use a tool...
Forum: Bioinformatics 06-14-2010, 11:38 AM
Replies: 7
Views: 4,621
Posted By Bio.X2Y
As I think about it, the second one seems to make...

As I think about it, the second one seems to make the most sense - "region of the sequence that remains after clipping".

Thanks for your input everyone.
Forum: Bioinformatics 06-14-2010, 11:15 AM
Replies: 7
Views: 4,621
Posted By Bio.X2Y
Thanks guys. lh3, I'm afraid I still find...

Thanks guys.

lh3, I'm afraid I still find that a bit ambiguous -

does "clipped sequence" refer to the "sequence that is clipped" (implying the whole thing, including the clipped part) or the...
Forum: Bioinformatics 06-14-2010, 10:45 AM
Replies: 7
Views: 4,621
Posted By Bio.X2Y
Thanks mrawlins! I'm leaning towards that...

Thanks mrawlins! I'm leaning towards that interpretation too.

I'm trying to get a definitive stance since I'm in the process of writing some code that supports sam, and I'd prefer not to add...
Forum: Bioinformatics 06-14-2010, 10:01 AM
Replies: 7
Views: 4,621
Posted By Bio.X2Y
SAM Format - Hard Clip

Hiya,

I was wondering can shed light on the following question on the hard-clipping within the SAM format (I'm not able to pinpoint an answer in the spec):

If a query read aligns with H's on...
Forum: Bioinformatics 06-14-2010, 06:22 AM
Replies: 3
Views: 6,058
Posted By Bio.X2Y
samtools picard SamFormatConverter

Hi,

I'm trying to run SamFormatConverter to convert a BAM to a SAM, and I'm getting an error (see below).

The text suggests that samtools is trying to parse my BAM as a SAM. However, the file...
Forum: Bioinformatics 06-10-2010, 01:30 PM
Replies: 4
Views: 13,514
Posted By Bio.X2Y
Thanks sklages! I wasn't aware of qual files. ...

Thanks sklages! I wasn't aware of qual files.

kwtennis311, there seem to be some existing posts on this, you might find answers in this, e.g. http://seqanswers.com/forums/showthread.php?t=3730.
Forum: Bioinformatics 06-10-2010, 12:06 PM
Replies: 4
Views: 13,514
Posted By Bio.X2Y
You could use awk to create a simple fasta file...

You could use awk to create a simple fasta file from your fastq, e.g.

awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' my.fastq > my.fasta

However, I don't think it makes any sense to...
Forum: Illumina/Solexa 06-08-2010, 08:10 AM
Replies: 1
Views: 1,335
Posted By Bio.X2Y
It looks like whoever wrote the code just wanted...

It looks like whoever wrote the code just wanted to round the answer to the nearest whole number (since int() on its own always rounds down).

int(3.1) -> 3
int(3.5) -> 3
int(3.9) -> 3

by...
Showing results 1 to 25 of 46

 


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