Forum: Bioinformatics
01-04-2019, 11:18 AM
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Replies: 3
Views: 1,887
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Forum: Bioinformatics
05-25-2016, 01:14 PM
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Replies: 2
Views: 1,495
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...
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Forum: Bioinformatics
02-18-2016, 03:34 PM
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Replies: 6
Views: 8,503
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Forum: Bioinformatics
02-16-2016, 09:44 AM
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Replies: 6
Views: 8,503
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...
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Forum: Bioinformatics
02-12-2016, 10:28 AM
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Replies: 6
Views: 1,928
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Forum: Bioinformatics
01-30-2016, 08:41 AM
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Replies: 28
Views: 61,004
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...
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Forum: Bioinformatics
12-18-2015, 03:46 PM
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Replies: 38
Views: 8,736
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...
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Forum: Bioinformatics
12-18-2015, 02:40 PM
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Replies: 38
Views: 8,736
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Forum: Bioinformatics
12-18-2015, 02:12 PM
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Replies: 38
Views: 8,736
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...
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Forum: Bioinformatics
12-18-2015, 01:49 PM
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Replies: 38
Views: 8,736
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Forum: Bioinformatics
12-18-2015, 01:36 PM
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Replies: 38
Views: 8,736
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...
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Forum: Bioinformatics
12-18-2015, 12:05 PM
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Replies: 38
Views: 8,736
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Forum: Bioinformatics
12-10-2015, 05:42 AM
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Replies: 4
Views: 3,921
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...
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Forum: Bioinformatics
11-22-2015, 02:02 PM
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Replies: 3
Views: 1,884
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...
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Forum: Bioinformatics
10-28-2015, 11:40 AM
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Replies: 15
Views: 6,677
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Forum: Bioinformatics
10-28-2015, 11:31 AM
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Replies: 4
Views: 2,962
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...
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Forum: Bioinformatics
10-16-2015, 04:51 PM
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Replies: 2
Views: 1,867
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Forum: Bioinformatics
07-31-2015, 12:14 PM
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Replies: 57
Views: 36,579
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Forum: Bioinformatics
05-14-2015, 12:35 PM
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Replies: 10
Views: 5,159
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...
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Forum: Bioinformatics
04-11-2015, 05:24 PM
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Replies: 77
Views: 27,445
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...
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Forum: Bioinformatics
04-08-2015, 10:10 AM
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Replies: 77
Views: 27,445
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...
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Forum: Bioinformatics
04-02-2015, 08:54 AM
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Replies: 77
Views: 27,445
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...
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Forum: Bioinformatics
04-01-2015, 10:08 AM
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Replies: 77
Views: 27,445
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...
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Forum: Bioinformatics
03-31-2015, 02:41 PM
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Replies: 77
Views: 27,445
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),...
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Forum: Bioinformatics
03-31-2015, 07:26 AM
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Replies: 77
Views: 27,445
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...
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