Forum: Bioinformatics
04-02-2018, 07:45 PM
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Replies: 1
Views: 406
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Forum: Bioinformatics
04-02-2018, 05:55 PM
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Replies: 3
Views: 513
Hi leshkowitz,
What annotation is being...
Hi leshkowitz,
What annotation is being shown in your bed file? Seems to be very small regions, followed by a gene symbol. Does this file contain all the information that will be needed to...
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Forum: Bioinformatics
03-28-2018, 03:29 PM
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Replies: 3
Views: 513
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Forum: Bioinformatics
03-25-2018, 02:44 PM
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Replies: 5
Views: 684
P.S. I guess the best idea would be to change...
P.S. I guess the best idea would be to change your workflow so that spaces and parentheses are not introduced into the file names. If you use some linux programs for trimming or other processing,...
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Forum: Bioinformatics
03-25-2018, 02:37 PM
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Replies: 5
Views: 684
Hi thermophile,
I'd say the problem with the...
Hi thermophile,
I'd say the problem with the new file names are the extra space and the parentheses. The extra space makes it difficult for the 'cp' command to know what is the file to copy and...
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Forum: Bioinformatics
03-22-2018, 09:15 PM
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Replies: 5
Views: 684
Hi thermophile,
Can you give us the complete...
Hi thermophile,
Can you give us the complete name of the old and new fastq files?
The first line in that script is where the variable 'f' is assigned to each of the file names, so it might be...
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Forum: Bioinformatics
01-24-2018, 01:12 PM
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Replies: 3
Views: 472
Hi lac302,
Well, you could do something like...
Hi lac302,
Well, you could do something like this:
for j in *reads.fq; do deinterleave_fastq.sh < $j $(basename $j .fq).F.fq $(basename $j .fq).R.fq [compress]; done
It's still a bit tricky...
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Forum: Bioinformatics
01-24-2018, 01:06 PM
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Replies: 1
Views: 326
Hi M,
In python, whitespace is very...
Hi M,
In python, whitespace is very important - this is how code blocks are separated ("indentation level" in the error). I'd guess that when you copy and pasted the script, the spaces or tabs...
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Forum: Bioinformatics
01-23-2018, 08:14 PM
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Replies: 3
Views: 472
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Forum: Bioinformatics
01-22-2018, 01:13 PM
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Replies: 5
Views: 507
Excellent!
I was thinking you could...
Excellent!
I was thinking you could probably also do a copy (cp) rather than renaming the files:
for j in */; do cp $j/fastqjoin.join.fastq $(basename $j).fastq; done
This would leave the...
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Forum: Bioinformatics
01-21-2018, 02:16 PM
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Replies: 5
Views: 507
Hi j.cappellazzi,
I think the below should...
Hi j.cappellazzi,
I think the below should work for renaming your files if you're sure qiime won't do it for you, or complain later when all the files are renamed. Be careful though - I wouldn't...
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Forum: Bioinformatics
01-16-2018, 02:26 PM
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Replies: 2
Views: 606
Hi LM,
It might be worth trying to get...
Hi LM,
It might be worth trying to get access to a server if you're going to start processing larger data sets. Does your university maintain a bioinformatics server? Then you can just have a...
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Forum: Bioinformatics
01-16-2018, 02:19 PM
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Replies: 1
Views: 592
Hi Yvan,
I can recommend topGO...
Hi Yvan,
I can recommend topGO (http://bioconductor.org/packages/release/bioc/html/topGO.html) as an R package that will do GO enrichment for you on a non-model organism. You basically just...
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Forum: Bioinformatics
12-13-2017, 02:31 PM
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Replies: 3
Views: 412
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Forum: Bioinformatics
12-13-2017, 02:08 PM
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Replies: 3
Views: 412
Hi dimo,
Are you analyzing this data on a...
Hi dimo,
Are you analyzing this data on a linux machine? The following sed command should do what you want for the first case:
sed "s/\(NB.*\)\(\s.*+\)\(.*\)/\1:\3\2\3/g" original_file >...
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Forum: RNA Sequencing
12-12-2017, 03:27 PM
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Replies: 1
Views: 824
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Forum: Bioinformatics
12-06-2017, 01:20 PM
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Replies: 7
Views: 662
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Forum: Bioinformatics
12-05-2017, 03:13 PM
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Replies: 9
Views: 870
I think it searches for that file from your...
I think it searches for that file from your current directory (not from the trimmomatic folder). You could put the adapter file in the same folder as your raw reads, then change that part of your...
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Forum: Bioinformatics
12-05-2017, 02:44 PM
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Replies: 7
Views: 662
#!/usr/bin/env python
# python 3
# take...
#!/usr/bin/env python
# python 3
# take kissplice output and get 'species-specific' SNPs
# Matthew J. Neave 06.12.2017
######################################
# the variables below can be...
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Forum: Bioinformatics
12-05-2017, 02:38 PM
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Replies: 7
Views: 662
Hi MGlenn,
yep, I think when it starts to...
Hi MGlenn,
yep, I think when it starts to get a bit complicated it's best to go for a python script. Then you also have a clean record of how it was done.
I've attached a script that should do...
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Forum: Bioinformatics
12-04-2017, 06:58 PM
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Replies: 7
Views: 662
Hi MGlenn,
Are you using linux for this...
Hi MGlenn,
Are you using linux for this analysis? You could print the lines containing that pattern using grep, for example:
grep "\(100.0|\)\{4\}\(0.0.\)\{4\}" your_input_file.txt
This...
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Forum: Bioinformatics
12-03-2017, 06:07 PM
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Replies: 3
Views: 509
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Forum: Bioinformatics
12-03-2017, 05:55 PM
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Replies: 3
Views: 509
Hi ML1975,
I just checked my latest protein...
Hi ML1975,
I just checked my latest protein BLAST databases. They also do not create a *.pal file, but they work fine with blastp or blastx. I think the *.pal files are only created if you have a...
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Forum: Bioinformatics
11-29-2017, 12:59 PM
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Replies: 5
Views: 577
hmm, well at least it's not just hanging!
...
hmm, well at least it's not just hanging!
Not sure why it's taking that long. If you've given cuffdiff all the threads '-p 40', I'd have thought that would be plenty. Maybe someone else has a...
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Forum: Bioinformatics
11-28-2017, 07:54 PM
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Replies: 5
Views: 577
Hi Capricy,
I recently used cuffdiff on 12...
Hi Capricy,
I recently used cuffdiff on 12 samples (bam sizes ~2Gb each) and it took 5-6 hours. This was using a server with 128Gb and 20 threads.
I'd say your process does seem a bit slow,...
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