Forum: Bioinformatics
02-12-2014, 01:28 PM
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Replies: 2
Views: 2,747
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...
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Forum: Bioinformatics
08-22-2013, 11:28 AM
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Replies: 1
Views: 1,789
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Forum: Bioinformatics
08-15-2013, 06:28 AM
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Replies: 13
Views: 13,245
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Forum: Bioinformatics
08-15-2013, 05:59 AM
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Replies: 13
Views: 13,245
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...
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Forum: Bioinformatics
08-15-2013, 03:27 AM
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Replies: 13
Views: 13,245
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...
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Forum: Bioinformatics
08-15-2013, 03:09 AM
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Replies: 3
Views: 1,235
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Forum: Bioinformatics
08-15-2013, 03:02 AM
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Replies: 1
Views: 1,171
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 ...
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Forum: Bioinformatics
06-07-2013, 08:17 AM
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Replies: 3
Views: 5,893
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Forum: Bioinformatics
06-07-2013, 03:29 AM
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Replies: 3
Views: 5,893
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Forum: Bioinformatics
05-29-2013, 04:09 AM
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Replies: 2
Views: 2,058
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)...
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Forum: Bioinformatics
05-11-2013, 05:20 AM
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Replies: 1
Views: 1,621
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...
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Forum: Bioinformatics
05-10-2013, 06:40 AM
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Replies: 0
Views: 1,025
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...
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Forum: RNA Sequencing
05-07-2013, 02:32 AM
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Replies: 3
Views: 1,618
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...
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Forum: RNA Sequencing
05-01-2013, 06:09 AM
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Replies: 3
Views: 1,618
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Forum: RNA Sequencing
05-01-2013, 05:07 AM
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Replies: 3
Views: 1,618
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:
...
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Forum: Bioinformatics
04-25-2013, 07:01 AM
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Replies: 12
Views: 5,168
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...
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Forum: Bioinformatics
04-25-2013, 03:34 AM
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Replies: 12
Views: 5,168
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...
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Forum: Bioinformatics
04-24-2013, 01:53 PM
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Replies: 12
Views: 5,168
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...
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Forum: Bioinformatics
04-24-2013, 03:36 AM
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Replies: 12
Views: 5,168
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...
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Forum: Bioinformatics
02-27-2013, 10:57 AM
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Replies: 10
Views: 6,631
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Forum: Bioinformatics
02-27-2013, 10:53 AM
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Replies: 17
Views: 33,075
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Forum: Bioinformatics
02-27-2013, 08:33 AM
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Replies: 17
Views: 33,075
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Forum: Bioinformatics
02-24-2013, 07:04 AM
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Replies: 17
Views: 33,075
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...
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Forum: Bioinformatics
02-22-2013, 08:05 AM
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Replies: 17
Views: 33,075
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...
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Forum: Bioinformatics
02-15-2013, 08:29 AM
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Replies: 1
Views: 1,817
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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