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Forum: Bioinformatics 06-08-2015, 05:11 AM
Replies: 5
Views: 1,358
Posted By A.N.Other
Please only post your issues in SeqAnswers OR...

Please only post your issues in SeqAnswers OR BioStars - it's a waste of people's time to respond to things that have already been answered elsewhere.

I was about to reply in BioStars, but I see...
Forum: Bioinformatics 11-26-2014, 02:53 AM
Replies: 3
Views: 8,219
Posted By A.N.Other
Pretty sure the OP has got past this by now, but...

Pretty sure the OP has got past this by now, but for thh32, it looks to me like it's an issue caused by a strange read ID that contains the '@' symbol at the start.

'@' at the start of a line...
Forum: Bioinformatics 10-13-2014, 02:54 AM
Replies: 6
Views: 1,435
Posted By A.N.Other
What format do you have the files in? Do you know...

What format do you have the files in? Do you know what (if any) processing the reads have had to get them into the state you have?
Forum: Bioinformatics 07-15-2014, 12:46 AM
Replies: 4
Views: 1,115
Posted By A.N.Other
Unless I'm missing something ......

Unless I'm missing something ... ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Rattus_norvegicus/Rnor_6.0/Primary_Assembly/assembled_chromosomes/FASTA/
Forum: Bioinformatics 01-31-2014, 12:43 AM
Replies: 10
Views: 4,464
Posted By A.N.Other
Ensembl will get you download whole legacy GTFs...

Ensembl will get you download whole legacy GTFs from their FTP (ftp://ftp.ensembl.org/pub/ --> choose the correct release --> gtf --> Mus musculus). You can filter out the miRNAs from the whole...
Forum: Bioinformatics 01-31-2014, 12:18 AM
Replies: 10
Views: 3,192
Posted By A.N.Other
Not necessarily quite that simple - I've had macs...

Not necessarily quite that simple - I've had macs center peaks in very strange places in some of my datasets in the past, and I'd agree that it's also a bit prone to elongating peaks. Depending on...
Forum: Bioinformatics 01-29-2014, 02:29 AM
Replies: 10
Views: 3,192
Posted By A.N.Other
Well chip peaks can legitimately vary from a few...

Well chip peaks can legitimately vary from a few 10s of bases to kilobases and beyond, so it's tricky to say what is 'correct' without knowing more about the dataset. What were you doing the chip...
Forum: Bioinformatics 01-29-2014, 01:30 AM
Replies: 10
Views: 3,192
Posted By A.N.Other
I should think MACS is the most widespread for...

I should think MACS is the most widespread for detection (excluding those that don't pay for something like Avadis or some other paid-for suite). Then MEME / MEMEchip for the analysis of the regions.
Forum: Bioinformatics 11-22-2013, 02:02 AM
Replies: 2
Views: 1,343
Posted By A.N.Other
I think you're probably going to need a slightly...

I think you're probably going to need a slightly more specialist tool than CLC to get you through this.

I suggest you also look over ShoRAH (Zagordi(2011)Bioinformatics) and V-Phaser...
Forum: Bioinformatics 09-12-2013, 01:08 AM
Replies: 8
Views: 3,011
Posted By A.N.Other
That you upload your large dataset to in order...

That you upload your large dataset to in order for the server to allow you to BLAST it? Is there any particular reason you can't download the BLAST+ suite and do it locally?
Forum: Bioinformatics 08-28-2013, 12:04 AM
Replies: 4
Views: 3,529
Posted By A.N.Other
The user manual is here ......

The user manual is here ... http://www.ncbi.nlm.nih.gov/books/NBK1763/
Forum: Bioinformatics 08-27-2013, 11:52 PM
Replies: 4
Views: 3,529
Posted By A.N.Other
Assuming you're doing it locally and have...

Assuming you're doing it locally and have downloaded BLAST+, then you should be using the blastn program with the "-task dc-megablast" flag.
Forum: Bioinformatics 07-30-2013, 05:27 AM
Replies: 4
Views: 1,896
Posted By A.N.Other
Quite possible. If you are behind a proxy...

Quite possible.

If you are behind a proxy server, are you configured to go through it? What's the contents of your /etc/environment ?

You can add the following lines to it ... obviously...
Forum: Bioinformatics 07-30-2013, 03:52 AM
Replies: 4
Views: 1,451
Posted By A.N.Other
As above, megablast is a search algorithm...

As above, megablast is a search algorithm implemented by in the NCBI BLAST+ tools. It's the default algorithm used in BLASTn, in fact, rather than 'blastn' itself.
Forum: Bioinformatics 06-20-2013, 08:21 AM
Replies: 8
Views: 1,721
Posted By A.N.Other
Do things other than IFNg behave as predicted -...

Do things other than IFNg behave as predicted - is this just isolated to this gene or is it a global issue? Check out some stuff in the same pathway. Could be that you have a mismatched genome and...
Forum: Bioinformatics 06-11-2013, 07:14 AM
Replies: 6
Views: 2,180
Posted By A.N.Other
It's a pretty cryptic error message, and I...

It's a pretty cryptic error message, and I haven't come across it myself. Things you might look into:

Was the file generated on a unix system? -- I'm thinking windows \r\n linebreaks (as opposed...
Forum: Bioinformatics 06-11-2013, 06:38 AM
Replies: 6
Views: 2,180
Posted By A.N.Other
Have you actually checked to ensure the format of...

Have you actually checked to ensure the format of the input fasta file? Have a 5sec visual inspection of it with a viewer like less.
Forum: Bioinformatics 03-26-2013, 03:35 AM
Replies: 7
Views: 2,457
Posted By A.N.Other
I would normally use: makeblastdb -in...

I would normally use:

makeblastdb -in <in_fa_file> -input_type fasta -title <title> -out <out_file>

-input_type defaults to fasta anyway, so the only issue I can see with your command is that...
Forum: Bioinformatics 03-22-2013, 02:56 AM
Replies: 3
Views: 3,133
Posted By A.N.Other
Do you have any proxy settings configured that...

Do you have any proxy settings configured that might be interfering with the program accessing the running server?

Add the following to /etc/environment and see if that solves it.
...
Forum: Bioinformatics 03-19-2013, 09:50 AM
Replies: 12
Views: 2,241
Posted By A.N.Other
Noticed you want to do it for a list of kmers. ...

Noticed you want to do it for a list of kmers. Assuming you have them in a text file, 1 per line, then this will pull out everything at once for you:


from sys import argv, version_info
from...
Forum: Bioinformatics 03-19-2013, 09:22 AM
Replies: 12
Views: 2,241
Posted By A.N.Other
Sorry, just changed it again, actually. Much...

Sorry, just changed it again, actually. Much faster now - I was doing it in a daft way as had just pulled it together for you from separate scripts.
Forum: Bioinformatics 03-19-2013, 09:03 AM
Replies: 12
Views: 2,241
Posted By A.N.Other
Looks like you have it sorted. Nevertheless, for...

Looks like you have it sorted. Nevertheless, for others doing this, here's a 2 minute python (v2 or 3) that will do the same with fastq or fasta (single line sequences). Very quick so no...
Forum: Bioinformatics 03-04-2013, 08:02 AM
Replies: 7
Views: 1,675
Posted By A.N.Other
You might have more long changing the -task flag...

You might have more long changing the -task flag to blastn-short. Default is megablast, which isn't optimised for finding things that small.

"blastn -help" to get the command line options.
Forum: Bioinformatics 07-09-2012, 02:37 AM
Replies: 14
Views: 4,855
Posted By A.N.Other
Setting the debug flags for cycle 9 within the...

Setting the debug flags for cycle 9 within the ProcessRepeats script doesn't shed any light on the issue for me. Execution stops after the following, with human ch22 for a fast run:


cycle 8...
Forum: Bioinformatics 07-08-2012, 02:03 PM
Replies: 14
Views: 4,855
Posted By A.N.Other
I too am having the same issue as above with...

I too am having the same issue as above with RepeatMasker stopping at Cycle 9 after identifying the elements in the input sequence. In fact, googling 'repeatmasker cycle 9' brought me to this thread...
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