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Forum: Bioinformatics 05-22-2018, 07:35 AM
Replies: 1
Views: 1,333
Posted By maubp
Looks like this issue? ...

Looks like this issue?
https://github.com/mummer4/mummer/issues/9

(I just ran into this error with mummer v3.23 and "gnuplot 5.0 patchlevel 5")
Forum: Bioinformatics 02-10-2017, 08:33 AM
Replies: 7
Views: 4,299
Posted By maubp
Here's a BLAST RBH tool I wrote earlier in...

Here's a BLAST RBH tool I wrote earlier in Python, which does consider duplicates and gives warnings about them:
https://github.com/peterjc/galaxy_blast/blob/master/tools/blast_rbh/blast_rbh.py
...
Forum: Bioinformatics 02-10-2017, 08:28 AM
Replies: 1
Views: 930
Posted By maubp
You could try a reference guided assembly,...

You could try a reference guided assembly, perhaps using MIRA?

You might want to first try mapping all the reads against the reference (with relaxed mapping settings) in order to divide the reads...
Forum: Bioinformatics 02-01-2017, 02:00 PM
Replies: 3
Views: 975
Posted By maubp
Sorry, you're right about the protein vs...

Sorry, you're right about the protein vs nucleotide focus.
Forum: Bioinformatics 02-01-2017, 08:58 AM
Replies: 3
Views: 975
Posted By maubp
This might be worth reading: Punta and Ofran...

This might be worth reading:

Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
or How To Use Sequence and Structure Information To Predict Protein
Function. PLoS Comput...
Forum: Bioinformatics 01-27-2017, 11:54 AM
Replies: 19
Views: 5,612
Posted By maubp
I believe the fairly new BLAST XML v2 output also...

I believe the fairly new BLAST XML v2 output also includes taxonomy information, if available.
Forum: Bioinformatics 10-31-2016, 03:11 AM
Replies: 8
Views: 1,894
Posted By maubp
I believe dayhan has soft trimmed bases at the...

I believe dayhan has soft trimmed bases at the edge of an NNNNN region in his reference, e.g.


ACGTNNNN Ref
ACGT---- Part mapped read, say ACGTGGTTwith 4 bases soft clipped, CIGAR 4M4S


To...
Forum: Bioinformatics 10-30-2016, 01:56 AM
Replies: 8
Views: 1,894
Posted By maubp
This is an interesting idea, I've wondered about...

This is an interesting idea, I've wondered about something similar in the context of how to visualise the soft clipping in an alignment viewer.

I can see how to do this in code. In addition to...
Forum: Bioinformatics 10-26-2016, 07:26 AM
Replies: 4
Views: 665
Posted By maubp
In which case its a near duplicate of @rvgill's...

In which case its a near duplicate of @rvgill's third thread http://seqanswers.com/forums/showthread.php?t=72192
Forum: Bioinformatics 10-26-2016, 07:10 AM
Replies: 1
Views: 596
Posted By maubp
This is a near duplicate of your other thread...

This is a near duplicate of your other thread where you have been given advice and help: http://seqanswers.com/forums/showthread.php?t=72083

The .nal file is a plain text file describing how to...
Forum: Bioinformatics 10-26-2016, 07:05 AM
Replies: 4
Views: 665
Posted By maubp
This is (almost) a duplicate of your other...

This is (almost) a duplicate of your other thread, where you have been given some help: http://seqanswers.com/forums/showthread.php?t=72083
Forum: Bioinformatics 10-26-2016, 06:55 AM
Replies: 8
Views: 1,807
Posted By maubp
Well spotted kmcarr, I had missed the...

Well spotted kmcarr, I had missed the sub-directory problem.
Forum: Bioinformatics 10-19-2016, 08:17 AM
Replies: 8
Views: 1,807
Posted By maubp
My guess is this line has an extra slash: ...

My guess is this line has an extra slash:

blastn -query HPV2-C2_E1.fasta -db MV1SDB_a/ -out testblastout.txt



Try:

blastn -query HPV2-C2_E1.fasta -db MV1SDB_a -out testblastout.txt
Forum: Bioinformatics 09-30-2016, 08:28 AM
Replies: 5
Views: 1,033
Posted By maubp
The NCBI BLAST website does a lot of parameter...

The NCBI BLAST website does a lot of parameter optimisation for you based things like query sequence length - the gap settings in particular are worth checking compared to the command line defaults.
Forum: Bioinformatics 08-29-2016, 02:48 AM
Replies: 14
Views: 5,743
Posted By maubp
Version which can be used on multiple files. In...

Version which can be used on multiple files. In order to keep the interface simple this just takes input filenames and writes the record to stdout, e.g.


$ python merge_gbk.py fileA.gbk fileB.gbk...
Forum: Bioinformatics 08-29-2016, 02:36 AM
Replies: 14
Views: 5,743
Posted By maubp
Thanks for emailing the files. Hmm. Where did...

Thanks for emailing the files. Hmm. Where did this "GenBank" files come from? That would be useful for us to know (e.g. for other people using the same tool), but right now my suggestion for setting...
Forum: Bioinformatics 08-29-2016, 02:17 AM
Replies: 14
Views: 5,743
Posted By maubp
Can you email me the two input files so I can...

Can you email me the two input files so I can test this locally (on GoogleMail - I'll message you via the forum)? Also please confirm which version of Biopython you have.
Forum: Bioinformatics 08-29-2016, 01:52 AM
Replies: 14
Views: 5,743
Posted By maubp
You need to use the forums's [ code ] and [ /code...

You need to use the forums's [ code ] and [ /code ] tags (without spaces) in order to preserve the white space - but this confirms you don't have proper GenBank files.

Biopython should be giving...
Forum: Bioinformatics 08-29-2016, 01:40 AM
Replies: 14
Views: 5,743
Posted By maubp
Normally the first line (the LOCUS line) of a...

Normally the first line (the LOCUS line) of a GenBank file says if the record is DNA or protein - and Biopython uses that information. If this failed I would expect this error on trying to save as...
Forum: Bioinformatics 07-30-2016, 01:18 PM
Replies: 2
Views: 1,431
Posted By maubp
Very few mappers have support for circular...

Very few mappers have support for circular genomes (e.g. CLC mapper), and worse, the SAM/BAM format does not handle this well. As suggested by Tristan, mapping to a doubled linear reference can be a...
Forum: General 04-10-2016, 10:34 AM
Replies: 2
Views: 857
Posted By maubp
For Brad's GFF code, you need...

For Brad's GFF code, you need https://github.com/chapmanb/bcbb/tree/master/gff
Forum: General 04-10-2016, 05:29 AM
Replies: 2
Views: 857
Posted By maubp
Unfortunately the Biopython website went down on...

Unfortunately the Biopython website went down on Friday, see http://mailman.open-bio.org/pipermail/biopython/2016-April/015909.html

We're working on it, and there's a possible migration in...
Forum: Bioinformatics 03-25-2016, 08:24 AM
Replies: 7
Views: 1,710
Posted By maubp
How did you install HTSeq and NumPy? My...

How did you install HTSeq and NumPy?

My guess is you have a mis-match between the version of NumPy installed, and the version that HTSeq expects (i.e. what it was compiled against).
Forum: Pacific Biosciences 03-11-2016, 05:34 AM
Replies: 13
Views: 2,313
Posted By maubp
Reply from the ENA DataSubs team: Please submit...

Reply from the ENA DataSubs team: Please submit the fastq or the native package but not both.

It looks like our first SMRT cell raw data has uploaded OK :)
Forum: Pacific Biosciences 03-10-2016, 08:24 AM
Replies: 13
Views: 2,313
Posted By maubp
In this case from two SMRT cells I have one FASTQ...

In this case from two SMRT cells I have one FASTQ file of filtered subreads used in the analysis, but I can easily split it up into one FASTQ file per run based on the read names.
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