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Forum: Bioinformatics 05-25-2016, 01:14 PM
Replies: 2
Views: 598
Posted By SES
I would recommend not doing this reformatting...

I would recommend not doing this reformatting approach, or at least proceeding with caution. With FASTA, you can be certain that the quality scores won't be used, but with a fake FASTQ you may be...
Forum: Bioinformatics 02-18-2016, 03:34 PM
Replies: 6
Views: 4,242
Posted By SES
This is very helpful, thanks. One question I have...

This is very helpful, thanks. One question I have would be about the merging that gffcompare does vs. the "stringtie --merge" method. It seems like "stringtie --merge" is the more appropriate method...
Forum: Bioinformatics 02-16-2016, 09:44 AM
Replies: 6
Views: 4,242
Posted By SES
I would try gffcompare...

I would try gffcompare (https://github.com/gpertea/gffcompare) (by the same author) instead of "stringtie --merge" because it seems to be more stringent. I have also experienced the same issue that...
Forum: Bioinformatics 02-12-2016, 10:28 AM
Replies: 6
Views: 908
Posted By SES
The database and driver are installed as a single...

The database and driver are installed as a single file with the Perl module DBD::SQLite, so if you can load that then it is unlikely a database dependency issue. I agree with the comment above that...
Forum: Bioinformatics 01-30-2016, 08:41 AM
Replies: 28
Views: 50,358
Posted By SES
I would use samtools: samtools bam2fq...

I would use samtools:

samtools bam2fq file.bam > file.fq

List of options:

Usage: samtools bam2fq [options...] <in.bam>
Options:
-0 FILE write paired reads flagged both or neither READ1...
Forum: Bioinformatics 12-18-2015, 03:46 PM
Replies: 38
Views: 2,555
Posted By SES
This is irrelevant now that the question is...

This is irrelevant now that the question is answered, but I can reproduce the "can't find getline..." error mentioned above that resulted from my first script.

The simple solution is to put "use...
Forum: Bioinformatics 12-18-2015, 02:40 PM
Replies: 38
Views: 2,555
Posted By SES
Great, thanks for the info. I'm creating a CentOS...

Great, thanks for the info. I'm creating a CentOS 6 image now to test your errors above.
Forum: Bioinformatics 12-18-2015, 02:12 PM
Replies: 38
Views: 2,555
Posted By SES
You must be giving the files in the wrong order...

You must be giving the files in the wrong order because it works for me. It needs to be "perl script.pl original.fas other.fas." Though, the approach I posted is odd since there is something wrong...
Forum: Bioinformatics 12-18-2015, 01:49 PM
Replies: 38
Views: 2,555
Posted By SES
Interesting, never seen that. What OS are you...

Interesting, never seen that. What OS are you using? To fix the Perl issue, replace this line:

return unless my $entry = $fh->getline;

with

return unless my $entry = <$fh>;

should do the...
Forum: Bioinformatics 12-18-2015, 01:36 PM
Replies: 38
Views: 2,555
Posted By SES
That is what the post above (#19...

That is what the post above (#19 (http://seqanswers.com/forums/showpost.php?p=186604&postcount=19)) produces. The question and expected results seem pretty simple, maybe you missed the previous post...
Forum: Bioinformatics 12-18-2015, 12:05 PM
Replies: 38
Views: 2,555
Posted By SES
Here is a simple script that uses an iterator to...

Here is a simple script that uses an iterator to fetch records by sequence. This would be likely faster and less error-prone than grep:

#!/usr/bin/env perl

use strict;
use warnings;
use...
Forum: Bioinformatics 12-10-2015, 05:42 AM
Replies: 4
Views: 1,809
Posted By SES
Prinseq handles paired-end files, it is not...

Prinseq handles paired-end files, it is not obsolete. You need to specify them correctly on the command line though with '-fastq' and '-fastq2' for each pair. It generates beautiful graphs of the...
Forum: Bioinformatics 11-22-2015, 02:02 PM
Replies: 3
Views: 1,034
Posted By SES
These are good things to ask the company since...

These are good things to ask the company since you paid for the product. It's not a bad idea to ask here but I think you'll get a faster and likely more accurate answer by just asking the blast2go...
Forum: Bioinformatics 10-28-2015, 11:40 AM
Replies: 15
Views: 4,822
Posted By SES
Still getting this error with the latest version?...

Still getting this error with the latest version? I haven't seen this one in particular but it could be that you don't have enough memory for the job. Can you run the commands with a smaller test...
Forum: Bioinformatics 10-28-2015, 11:31 AM
Replies: 4
Views: 2,011
Posted By SES
I think the problem is the way that the fasta...

I think the problem is the way that the fasta directory is specified and also the read IDs. Note that "22" and "chr22" are different and not compatible. Other than that, the order of the commands...
Forum: Bioinformatics 10-16-2015, 04:51 PM
Replies: 2
Views: 942
Posted By SES
This is a great question and I hope it gets more...

This is a great question and I hope it gets more attention.

I have used CNVnator for analyzing CNVs in plants and it works well. One criticism is the lack of documentation. There is no advice on...
Forum: Bioinformatics 07-31-2015, 12:14 PM
Replies: 55
Views: 26,209
Posted By SES
On the contrary, I think this is a solved problem...

On the contrary, I think this is a solved problem for the most part. There are at least two general solutions (Pairfq and bbtools) discussed above that work on multi-line fasta/q, compresed files,...
Forum: Bioinformatics 05-14-2015, 12:35 PM
Replies: 10
Views: 1,996
Posted By SES
Those are conflicting statements, you can't...

Those are conflicting statements, you can't accomplish not installing anything by installing something :). I think I know what you mean though, no external dependencies. We don't really need anything...
Forum: Bioinformatics 04-11-2015, 05:24 PM
Replies: 77
Views: 21,757
Posted By SES
That was my bad, one of the files was named...

That was my bad, one of the files was named incorrectly in the script. I fixed that typo and changed the command to use the curl method so we can rule out the installation being an issue. I ran the...
Forum: Bioinformatics 04-08-2015, 10:10 AM
Replies: 77
Views: 21,757
Posted By SES
I tried the whole process using the commands...

I tried the whole process using the commands above and did not find any issues. Here is the script: seqanswers163784.sh (https://gist.github.com/sestaton/09781a5ac8849753d6ed) (link to a gist, not a...
Forum: Bioinformatics 04-02-2015, 08:54 AM
Replies: 77
Views: 21,757
Posted By SES
Okay, we would need to see the command you used...

Okay, we would need to see the command you used to trim the files (and any other operations), as Brian mentioned above. That way we can try to reproduce the issue. One other thing to consider is that...
Forum: Bioinformatics 04-01-2015, 10:08 AM
Replies: 77
Views: 21,757
Posted By SES
This confirms that it is not an issue with any...

This confirms that it is not an issue with any program, and it is clearly an issue with the data. If you got things to work before, try to re-trace your process with this data set to find out where...
Forum: Bioinformatics 03-31-2015, 02:41 PM
Replies: 77
Views: 21,757
Posted By SES
The IDs are different, so I think this is a...

The IDs are different, so I think this is a different data set. Also, I think the same person asked this question on stackoverflow, where I answered it (http://stackoverflow.com/a/29190466/1543853),...
Forum: Bioinformatics 03-31-2015, 07:26 AM
Replies: 77
Views: 21,757
Posted By SES
This may be one issue, as these reads are not...

This may be one issue, as these reads are not proper fastq (records should start with "@"). Because this will likely cause issues with any downstream program, I would fix the format and then re-pair...
Forum: Bioinformatics 03-30-2015, 06:54 AM
Replies: 77
Views: 21,757
Posted By SES
Ah, thanks I missed that. The reads look normal...

Ah, thanks I missed that. The reads look normal to me, so I don't see a reason to add the pair info as I suggested above. Nothing jumps out at me as being problematic with the data or commands, but...
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