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Search: Posts Made By: neavemj
Forum: Bioinformatics 04-02-2018, 07:45 PM
Replies: 1
Views: 406
Posted By neavemj
I think you need to specify the output file. For...

I think you need to specify the output file. For example, add "-S new_file.sam" to the script.

Cheers,

Matt.
Forum: Bioinformatics 04-02-2018, 05:55 PM
Replies: 3
Views: 513
Posted By neavemj
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...
Forum: Bioinformatics 03-28-2018, 03:29 PM
Replies: 3
Views: 513
Posted By neavemj
What does the bed file look like? Maybe a...

What does the bed file look like? Maybe a combination of grep and awk could work?
Forum: Bioinformatics 03-25-2018, 02:44 PM
Replies: 5
Views: 684
Posted By neavemj
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,...
Forum: Bioinformatics 03-25-2018, 02:37 PM
Replies: 5
Views: 684
Posted By neavemj
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...
Forum: Bioinformatics 03-22-2018, 09:15 PM
Replies: 5
Views: 684
Posted By neavemj
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...
Forum: Bioinformatics 01-24-2018, 01:12 PM
Replies: 3
Views: 472
Posted By neavemj
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...
Forum: Bioinformatics 01-24-2018, 01:06 PM
Replies: 1
Views: 326
Posted By neavemj
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...
Forum: Bioinformatics 01-23-2018, 08:14 PM
Replies: 3
Views: 472
Posted By neavemj
Maybe you could loop over each of the interleaved...

Maybe you could loop over each of the interleaved files and run the script? Something like:

for j in *fastq; do deinterleave_fastq.sh $j *options; done

If you could tell me your directory...
Forum: Bioinformatics 01-22-2018, 01:13 PM
Replies: 5
Views: 507
Posted By neavemj
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...
Forum: Bioinformatics 01-21-2018, 02:16 PM
Replies: 5
Views: 507
Posted By neavemj
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...
Forum: Bioinformatics 01-16-2018, 02:26 PM
Replies: 2
Views: 606
Posted By neavemj
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...
Forum: Bioinformatics 01-16-2018, 02:19 PM
Replies: 1
Views: 592
Posted By neavemj
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...
Forum: Bioinformatics 12-13-2017, 02:31 PM
Replies: 3
Views: 412
Posted By neavemj
In that case, you can rearrange that sed command...

In that case, you can rearrange that sed command like so:

sed "s/\(NB.*\)\(\s.*+\)\(.*\)/\1\2\3\n\3/g" original_file > new_file

This is now saying 'insert a newline character (\n) before...
Forum: Bioinformatics 12-13-2017, 02:08 PM
Replies: 3
Views: 412
Posted By neavemj
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 >...
Forum: RNA Sequencing 12-12-2017, 03:27 PM
Replies: 1
Views: 824
Posted By neavemj
Hi tonup69, Might be best to post the actual...

Hi tonup69,

Might be best to post the actual error you are getting - why won't RNA Star accept your files?

Cheers,

Matt.
Forum: Bioinformatics 12-06-2017, 01:20 PM
Replies: 7
Views: 662
Posted By neavemj
Excellent, glad it worked ok! :) Best, ...

Excellent, glad it worked ok! :)

Best,

Matt.
Forum: Bioinformatics 12-05-2017, 03:13 PM
Replies: 9
Views: 870
Posted By neavemj
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...
Forum: Bioinformatics 12-05-2017, 02:44 PM
Replies: 7
Views: 662
Posted By neavemj
#!/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...
Forum: Bioinformatics 12-05-2017, 02:38 PM
Replies: 7
Views: 662
Posted By neavemj
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...
Forum: Bioinformatics 12-04-2017, 06:58 PM
Replies: 7
Views: 662
Posted By neavemj
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...
Forum: Bioinformatics 12-03-2017, 06:07 PM
Replies: 3
Views: 509
Posted By neavemj
hmm, I'm afraid I haven't heard of that program. ...

hmm, I'm afraid I haven't heard of that program.

Good luck!

Matt.
Forum: Bioinformatics 12-03-2017, 05:55 PM
Replies: 3
Views: 509
Posted By neavemj
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...
Forum: Bioinformatics 11-29-2017, 12:59 PM
Replies: 5
Views: 577
Posted By neavemj
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...
Forum: Bioinformatics 11-28-2017, 07:54 PM
Replies: 5
Views: 577
Posted By neavemj
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,...
Showing results 1 to 25 of 53

 


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