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Search: Posts Made By: chris
Forum: Bioinformatics 01-21-2013, 01:56 AM
Replies: 5
Views: 2,394
Posted By chris
Sure, its: bowtie2 --threads 4 -q...

Sure, its:


bowtie2 --threads 4 -q --sensitive --end-to-end --phred33 -x /db/bowtie2/Hsapiens68 -1 fastq_file1 -2 fastq_file1 -S out.sam
Forum: Bioinformatics 01-21-2013, 01:52 AM
Replies: 4
Views: 1,816
Posted By chris
I thought this was a dead thread so didn't...

I thought this was a dead thread so didn't update.

Problem is/was the '-I' switch in bwa. It doesn't work with newer sanger fastq format files produced with Illumina pipeline v1.8+: remove switch...
Forum: Bioinformatics 10-21-2012, 01:06 PM
Replies: 5
Views: 2,394
Posted By chris
Great. Thanks.

Great. Thanks.
Forum: Bioinformatics 10-19-2012, 09:18 AM
Replies: 5
Views: 2,394
Posted By chris
On/off target rate for whole exome data

Hi all,

I've some human exome data, which I've aligned with bowtie2 as bwa doesn't work (see this post (http://seqanswers.com/forums/showthread.php?t=24113)).

Using samtools flagstat I can see...
Forum: Bioinformatics 10-19-2012, 08:52 AM
Replies: 4
Views: 1,816
Posted By chris
Bump. Am I the only one seeing this?

Bump. Am I the only one seeing this?
Forum: Bioinformatics 10-15-2012, 01:29 AM
Replies: 4
Views: 1,816
Posted By chris
Problematic Fastq qualities with BWA

Hi all,

I'm having problems running BWA (0.5.9-r16 and 0.6.2) on some new whole exome data.

The initial alignment runs fine (it seems) but when I want to create a SAM file with 'bwa sampe' it...
Forum: Bioinformatics 06-11-2012, 08:16 AM
Replies: 14
Views: 5,619
Posted By chris
The tophat run finished after 64hrs and a quick...

The tophat run finished after 64hrs and a quick look in IGV seems to show very similar results to STAR.

The most obvious difference seems to be that STAR reports pairs even when the pair distance...
Forum: Bioinformatics 06-08-2012, 01:20 PM
Replies: 5
Views: 2,483
Posted By chris
Yup. Been there... I had some genes going from...

Yup. Been there... I had some genes going from p=1e-74 to p=0.01. I suggest you check the significant genes and see if they look believable in relation to the raw data. Particularly watch out for...
Forum: Bioinformatics 06-08-2012, 08:28 AM
Replies: 6
Views: 1,883
Posted By chris
It would help if you stated the name of the...

It would help if you stated the name of the database you used on NCBI. Then a judgement can be made as to whether you're comparing like with like.
Forum: Bioinformatics 06-08-2012, 08:00 AM
Replies: 6
Views: 1,883
Posted By chris
Not to me. Those scores are very poor and...

Not to me. Those scores are very poor and probably the worst that can be reported by BLAST for your database. So, although they are *hits* I doubt they are meaningful.



I suspect your searching...
Forum: Bioinformatics 06-08-2012, 07:47 AM
Replies: 2
Views: 2,564
Posted By chris
OK. It looks like it died trying to sort eight...

OK. It looks like it died trying to sort eight BAM files at the same time and then merging them into one. I'll try and run those steps separately and see how that goes...

Grazie mille
Forum: Bioinformatics 06-08-2012, 02:55 AM
Replies: 14
Views: 5,619
Posted By chris
As an update the job finished in 9 days - with an...

As an update the job finished in 9 days - with an 'out of memory' error :mad:

I've started a new thread regarding the possibility of restarting the job a the point of failure:...
Forum: Bioinformatics 06-08-2012, 02:48 AM
Replies: 2
Views: 2,564
Posted By chris
Tophat2 job fails with an out of memory error - how to restart?

I've had a long running tophat2 end with an error after 9 nine days:



Is there anyway to restart it at the point of failure on a machine with more memory rather than waiting another 9 nine...
Forum: Bioinformatics 05-22-2012, 08:33 AM
Replies: 14
Views: 5,619
Posted By chris
:D If only...

:D

If only...
Forum: Bioinformatics 05-22-2012, 08:23 AM
Replies: 1
Views: 1,329
Posted By chris
If all you're after is information on two known...

If all you're after is information on two known miRNAs then you need to go the miRBase website: http://www.mirbase.org

You can search the database by miRNA name or by sequence.

No need for any...
Forum: Bioinformatics 05-22-2012, 08:16 AM
Replies: 14
Views: 5,619
Posted By chris
Just noticed that the file...

Just noticed that the file tophat_out/logs/segment_juncs.log is being updated every few hours. 17 chromosomes done so far, only ~60 to go... :(
Forum: Bioinformatics 05-21-2012, 06:33 AM
Replies: 14
Views: 5,619
Posted By chris
It really isn't that many reads. It's equivalent...

It really isn't that many reads. It's equivalent to just one lane of HiSeq.



Thanks. I'll give it a try.



Was that paired-end data? What parameters were you using?
Forum: Bioinformatics 05-21-2012, 05:27 AM
Replies: 14
Views: 5,619
Posted By chris
Thanks for the reply. You're right it is...

Thanks for the reply.

You're right it is very disconcerting. There's nothing in the output or log files or even in the tmp/ directory to indicate anything is happening. The only indicator is the...
Forum: Bioinformatics 05-21-2012, 02:38 AM
Replies: 14
Views: 5,619
Posted By chris
Exclamation How long to wait for Tophat2 to finish?

Hi all,

I'm trying to run tophat2 on a three paired-end datasets against hg19, but it has taken three days so far! How long do typical runs take for other people??

I've run it with 8 threads on...
Forum: Bioinformatics 11-30-2011, 08:28 AM
Replies: 9
Views: 5,905
Posted By chris
You feel my pain :( We've had a similar...

You feel my pain :(

We've had a similar issue with DESeq and EdgeR, here. What I do is try and look at the 'significant' genes and check that the expression values agree with what the program...
Forum: Bioinformatics 09-07-2011, 01:04 AM
Replies: 47
Views: 13,233
Posted By chris
I'm not calling him names, just the project...

I'm not calling him names, just the project planners.

Are many projects really this short-sighted?? I know I'm lucking working in a dept which values Bioinformatics and backs that up with a 500...
Forum: Bioinformatics 09-06-2011, 07:56 AM
Replies: 47
Views: 13,233
Posted By chris
This is idiotic! You're spending >$50K on...

This is idiotic! You're spending >$50K on sequencing but can't spend more than $2K on the analysis hardware, you're really shooting yourself in the foot.

The sequencing is the easy bit and doing...
Forum: Bioinformatics 08-24-2011, 07:08 AM
Replies: 11
Views: 6,606
Posted By chris
Yup, I see that's the issue, but I thought DESeq...

Yup, I see that's the issue, but I thought DESeq took consideration of large variance in calculating the p-values. I'll take a look at the percentiles and see what difference it makes.
Forum: Bioinformatics 08-23-2011, 08:30 AM
Replies: 11
Views: 6,606
Posted By chris
Yup, they're both adjusted for multiple...

Yup, they're both adjusted for multiple hypothesis testing using the BH method.
Forum: Bioinformatics 08-23-2011, 07:54 AM
Replies: 11
Views: 6,606
Posted By chris
Here's an example of a gene in my data...

Here's an example of a gene in my data (normalised counts):

cond1 (6 reps): 32.94 52.71 53.99 33.60 38.03 49.97
cond2 (4reps): 53.09 42.20 1.02 0.64

Limma gives an...
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