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Forum: Bioinformatics 02-12-2014, 12:28 PM
Replies: 2
Views: 2,617
Posted By nr23
Gene Ontology in non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I...
Forum: Bioinformatics 08-22-2013, 10:28 AM
Replies: 1
Views: 1,711
Posted By nr23
Q values in cuffdiff with 2 biological replicates

I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change...
Forum: Bioinformatics 08-15-2013, 05:28 AM
Replies: 13
Views: 13,045
Posted By nr23
Ah - ok. Is there a quick way to check the...

Ah - ok. Is there a quick way to check the permission for the directory tree?
Forum: Bioinformatics 08-15-2013, 04:59 AM
Replies: 13
Views: 13,045
Posted By nr23
The permissions seem good on 'merged.gtf' ...

The permissions seem good on 'merged.gtf'

-rw-r--r-- 1 user acc 94M 2013-08-15 10:16 merged.gtf

I've write-enabled both files, but I've never had to do this before, and this doesn't fix the...
Forum: Bioinformatics 08-15-2013, 02:27 AM
Replies: 13
Views: 13,045
Posted By nr23
I have the same problem as above: I've run the...

I have the same problem as above: I've run the exact same script (with different .bams) many times without error. Now it fufuses to run with:

cuffdiff: /lib64/libz.so.1: no version information...
Forum: Bioinformatics 08-15-2013, 02:09 AM
Replies: 3
Views: 1,181
Posted By nr23
I also experienced this problem a while back. It...

I also experienced this problem a while back. It is incredibly sloppy for them to have neglected this from my point of view. I use trimmomatic and have found it better on all fronts!

N
Forum: Bioinformatics 08-15-2013, 02:02 AM
Replies: 1
Views: 1,108
Posted By nr23
Cuffdiff problems

I'm running Cuffdiff v2.1.1 and am running into problems:

My script is:

cuffdiff -p 12 -o ./diff_out -b /ichec/work/nglif015b/nick/bowtie/bowtie-indexes/Laevis_7/Xl7.fasta -L con,smo ...
Forum: Bioinformatics 06-07-2013, 07:17 AM
Replies: 3
Views: 5,754
Posted By nr23
So this isn't actually a bad thing, so to speak?...

So this isn't actually a bad thing, so to speak? If that's the case, I would have expected to see this sort of result quite frequently, where one condition has 0 reads mapping to a given gene and the...
Forum: Bioinformatics 06-07-2013, 02:29 AM
Replies: 3
Views: 5,754
Posted By nr23
Cuffdiff output shows log2(fold change) as infinite

Hi, I've compared two conditions in cuffdiff (2 reps each). On examining the output, I see in the gene_exp.diff file that some of the XLOC features show 'NOTEST' under the status column, and '-inf'...
Forum: Bioinformatics 05-29-2013, 03:09 AM
Replies: 2
Views: 1,924
Posted By nr23
When to merge specify replicates

Hi,

I've got RNA-Seq data (pe 100bp) from several biological replicates and 11 different conditions and want to compare DE between conditions.

I'm using the tuxedo suite (tophat, cufflinks)...
Forum: Bioinformatics 05-11-2013, 04:20 AM
Replies: 1
Views: 1,562
Posted By nr23
Cummerbund get locus

Hi,

I've mapped PE RNA-Seq reads to a Unigene database, with each scaffold representing an expressed gene, and annotated with the gene information (I don't have an annotation.gtf file).

I've...
Forum: Bioinformatics 05-10-2013, 05:40 AM
Replies: 0
Views: 966
Posted By nr23
How does cufflinks sort scaffolds?

Hi,

I'm trying to map RNA-Seq reads to a Unigene (EST) database containing 30,000+ scaffolds. I've blasted each scaffold (gene) and annotated them with the blast results, so for example the first...
Forum: RNA Sequencing 05-07-2013, 01:32 AM
Replies: 3
Views: 1,544
Posted By nr23
Hi, I re-ran the manual sort $ sort -k 3,3...

Hi,

I re-ran the manual sort $ sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted on my sam files and cufflinks runs ok. It takes ~ 4 hours per condition (~80M 90bp pe reads) - which seems...
Forum: RNA Sequencing 05-01-2013, 05:09 AM
Replies: 3
Views: 1,544
Posted By nr23
Hi, Yes I did today. However, I'm aligning...

Hi,

Yes I did today. However, I'm aligning to a Unigene reference with 30k odd sequences, so I have headers that are too large for v.1. - I'll give v.2.0.2 a go.

Thanks,

N
Forum: RNA Sequencing 05-01-2013, 04:07 AM
Replies: 3
Views: 1,544
Posted By nr23
Cufflinks sorting Error

Hi,

I've used Cufflinks a load of times, with both sorted.bam alignments from tophat and Stampy. Even though my .bam files are sorted (samtools sort) I get this error when running cufflinks:

...
Forum: Bioinformatics 04-25-2013, 06:01 AM
Replies: 12
Views: 5,011
Posted By nr23
OK - think I cracked it: my (@gi,...

OK - think I cracked it:


my (@gi, @number, @gb, @id, @name, @test);
my @heads = split('\n', $hits);
my $increment = 0;
foreach (@heads) {
my @split = split('\|');
++$increment;
push...
Forum: Bioinformatics 04-25-2013, 02:34 AM
Replies: 12
Views: 5,011
Posted By nr23
Great - thanks. What I really want to do is...

Great - thanks.

What I really want to do is change the field i've called 'id' for each header. I would do this by looping through each element in the id array and ++$some_counter and reassemble...
Forum: Bioinformatics 04-24-2013, 12:53 PM
Replies: 12
Views: 5,011
Posted By nr23
Thanks guys for the suggestions. Westerman...

Thanks guys for the suggestions.

Westerman - sorry I should have been clearer: I actually DO want to isolate all parts of all headers so that I can for example modify (or delete) individual...
Forum: Bioinformatics 04-24-2013, 02:36 AM
Replies: 12
Views: 5,011
Posted By nr23
Array of arrays in perl

Hi everyone,

I'm trying to write a perl programme that will split up a .fasta header:

gi|4140243|dbj|AB022087.1|_Xenopus_laevis_mRNA_for_cytochrome_P450,_complete_cds,_clone_MC1

Into its...
Forum: Bioinformatics 02-27-2013, 09:57 AM
Replies: 10
Views: 6,444
Posted By nr23
Did you manage to write that script Bueller? I'm...

Did you manage to write that script Bueller? I'm mid way through doing something similar and would appreciate any perl tips...
Forum: Bioinformatics 02-27-2013, 09:53 AM
Replies: 17
Views: 31,490
Posted By nr23
Awesome - thanks a lot! That's really cleared...

Awesome - thanks a lot! That's really cleared things up.
Forum: Bioinformatics 02-27-2013, 07:33 AM
Replies: 17
Views: 31,490
Posted By nr23
Thanks guys - I think I've got it down now: ...

Thanks guys - I think I've got it down now:

this suggestion works well:

blastn -query your.fa -db your_db.fa -outfmt 6 | sort -k1,1 -k12,12nr -k11,11n | sort -u -k1,1 --merge >...
Forum: Bioinformatics 02-24-2013, 06:04 AM
Replies: 17
Views: 31,490
Posted By nr23
What's the top HSP? I've made some progress...

What's the top HSP?

I've made some progress using:

blastn -db trop -query blast.fa -outfmt 6 -max_target_seqs 1 -num_alignments 1 -num_descriptions 1 -out results.out

which makes isolating...
Forum: Bioinformatics 02-22-2013, 07:05 AM
Replies: 17
Views: 31,490
Posted By nr23
Blastn to return only top hit

Hi,

I'm trying to use Blastn to blast an entire Unigene file (only cds) in order to get gene names for my reference sequence. I then want to attach these gene names to the FASTA sequence and use...
Forum: Bioinformatics 02-15-2013, 07:29 AM
Replies: 1
Views: 1,730
Posted By nr23
samtools faidx

Hi,

I've aligned RNA-Seq PE reads to X.laevis unigene EST database and have generated DE gene lists with cuffdiff. I assumed that there was no annotation file but have just noticed that the .fa...
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