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Search: Posts Made By: neavemj
Forum: Bioinformatics 10-30-2018, 03:42 PM
Replies: 1
Views: 305
Posted By neavemj
Hi Morko, I would recommend MAKER...

Hi Morko,

I would recommend MAKER (http://www.yandell-lab.org/software/maker.html). This is an annotation pipeline that will allow you to use homology-based predictions from closely related...
Forum: Bioinformatics 09-30-2018, 09:28 PM
Replies: 5
Views: 923
Posted By neavemj
Hi CarnifexRex! That's getting a bit...

Hi CarnifexRex!

That's getting a bit trickier because you want to do something with the 'next' line as well as the matched line. Here is how I would do it, although I think there are probably...
Forum: Bioinformatics 07-10-2018, 03:44 PM
Replies: 3
Views: 725
Posted By neavemj
Hmm, yep might need a bit of digging. It does...

Hmm, yep might need a bit of digging. It does seem that the script is requiring headers that look like NCBI / uniprot, e.g:

<Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>

Perhaps when you...
Forum: Bioinformatics 07-09-2018, 05:03 PM
Replies: 3
Views: 725
Posted By neavemj
Hi Irene, That error is because python is...

Hi Irene,

That error is because python is trying to get the second item in a list but the list only contains one item. Looking at the code (line 299), it appears that the script is trying to make...
Forum: Bioinformatics 06-11-2018, 04:59 PM
Replies: 1
Views: 540
Posted By neavemj
Hi Lina, I think you might be trying to give...

Hi Lina,

I think you might be trying to give your forward reads twice to both the in1 and in2 arguments. Maybe your in2 argument should be:

in2=${R2}

I guess bbmap checks that the F and R...
Forum: Bioinformatics 04-02-2018, 08:45 PM
Replies: 1
Views: 680
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, 06:55 PM
Replies: 3
Views: 712
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, 04:29 PM
Replies: 3
Views: 712
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, 03:44 PM
Replies: 5
Views: 826
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, 03:37 PM
Replies: 5
Views: 826
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, 10:15 PM
Replies: 5
Views: 826
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, 02:12 PM
Replies: 3
Views: 859
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, 02:06 PM
Replies: 1
Views: 590
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, 09:14 PM
Replies: 3
Views: 859
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, 02:13 PM
Replies: 5
Views: 652
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, 03:16 PM
Replies: 5
Views: 652
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, 03:26 PM
Replies: 2
Views: 1,165
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, 03:19 PM
Replies: 1
Views: 897
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, 03:31 PM
Replies: 5
Views: 923
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, 03:08 PM
Replies: 5
Views: 923
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, 04:27 PM
Replies: 1
Views: 1,004
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, 02:20 PM
Replies: 7
Views: 973
Posted By neavemj
Excellent, glad it worked ok! :) Best, ...

Excellent, glad it worked ok! :)

Best,

Matt.
Forum: Bioinformatics 12-05-2017, 04:13 PM
Replies: 9
Views: 1,464
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, 03:44 PM
Replies: 7
Views: 973
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, 03:38 PM
Replies: 7
Views: 973
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...
Showing results 1 to 25 of 58

 


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