Forum: Bioinformatics
05-13-2014, 08:05 AM
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Replies: 1
Views: 5,606
You must install 'gfortran' package, then...
You must install 'gfortran' package, then ./configure, then make. I had the same problem and it worked for me. I got it from here:
http://r.789695.n4.nabble.com/R-3-0-1-g77-errors-td4676434.html
...
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Forum: Bioinformatics
03-10-2010, 07:34 AM
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Replies: 42
Views: 112,094
Thanks a lot. By "these are not currenly...
Thanks a lot. By "these are not currenly standardized" do you mean that values for this tags are not pre-defined (e.g., '454', 'Illumina', and 'solid' for PL tag) so that they can be freely selected?
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Forum: Bioinformatics
03-10-2010, 04:33 AM
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Replies: 42
Views: 112,094
In this wike, one can found the following...
In this wike, one can found the following commands:
perl -e 'print "@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illumina\n@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"' > rg.txt
samtools merge -rh rg.txt - ga.bam...
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Forum: Bioinformatics
02-25-2010, 09:40 AM
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Replies: 78
Views: 33,941
I think I've found a minor bug in an error...
I think I've found a minor bug in an error message raised by solid2fastq.pl script distributed with bwa when it founds a mismatching name in the .csfasta and .qual input files:
The following line...
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Forum: RNA Sequencing
02-23-2010, 01:01 AM
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Replies: 21
Views: 19,526
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Forum: RNA Sequencing
02-22-2010, 06:04 AM
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Replies: 21
Views: 19,526
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Forum: RNA Sequencing
02-22-2010, 04:04 AM
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Replies: 21
Views: 19,526
Is it possible to get these scripts? I've also...
Is it possible to get these scripts? I've also written one of them, but I'm a biologist and not very experienced in optimizing memory resources in my code, so that my script takes days to finish and,...
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Forum: RNA Sequencing
02-18-2010, 09:25 AM
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Replies: 21
Views: 19,526
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Forum: Bioinformatics
02-16-2010, 08:45 AM
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Replies: 7
Views: 4,625
I've found such a tool in the bin directory of...
I've found such a tool in the bin directory of Corona_Lite distribution. Its name is encodeFasta.py. It could be used for several interconversions (color-space, double-encoded, nucleotide-space).
...
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Forum: Bioinformatics
02-16-2010, 06:59 AM
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Replies: 7
Views: 4,625
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Forum: Bioinformatics
02-13-2010, 03:06 PM
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Replies: 78
Views: 33,941
Hi, Lisa. As you can see in previous posts, it...
Hi, Lisa. As you can see in previous posts, it seems to be related to a wrong construction of the fastq file by the solid2fastq (or similar) script. At least in my case, using the last solidfastq...
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Forum: Bioinformatics
02-10-2010, 08:16 AM
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Replies: 21
Views: 6,389
Maybe this is not true, since I have a 250,000...
Maybe this is not true, since I have a 250,000 reads fastq file producing the memory corruption error, whereas the two 125,000 reads fastq files obtained by splitting it did not cause the error....
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Forum: Bioinformatics
02-10-2010, 06:39 AM
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Replies: 21
Views: 6,389
I think BFAST author follows closely this...
I think BFAST author follows closely this forum...
BTW, it seems that BFAST does not like some read/s, so that memory corruption error only appears in subsets of reads having it/them. This would...
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Forum: Bioinformatics
02-10-2010, 05:44 AM
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Replies: 78
Views: 33,941
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Forum: Bioinformatics
02-10-2010, 05:33 AM
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Replies: 21
Views: 6,389
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Forum: Bioinformatics
02-10-2010, 03:40 AM
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Replies: 78
Views: 33,941
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Forum: Bioinformatics
02-09-2010, 01:43 PM
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Replies: 5
Views: 2,030
In BFAST book, you can find the following: 'If...
In BFAST book, you can find the following: 'If you wish to have a secondary set of indexes, which are used if no matches are found in the main set of indexes, use the -I option'. So, I thought that...
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Forum: Bioinformatics
02-09-2010, 09:57 AM
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Replies: 5
Views: 2,030
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Forum: Bioinformatics
02-09-2010, 09:54 AM
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Replies: 5
Views: 2,030
BFAST error in FindMatchesInIndexSet function
Hi all,
I successfully went along the first steps of BFAST pipeline, including the indexes creation, but got the below copied error when running 'bfast match' step with the following command for a...
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Forum: Bioinformatics
02-08-2010, 04:43 AM
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Replies: 9
Views: 7,022
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Forum: Bioinformatics
02-08-2010, 02:47 AM
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Replies: 78
Views: 33,941
solved
In my case, using the solid2fastq.pl shipped with the SVN above indicated solved the problems: fastq file is correctly produced (read names are properly trimmed), and using that fastq file does not...
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Forum: Bioinformatics
02-08-2010, 02:30 AM
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Replies: 9
Views: 7,022
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Forum: Bioinformatics
02-05-2010, 02:52 PM
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Replies: 78
Views: 33,941
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Forum: Bioinformatics
02-05-2010, 06:21 AM
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Replies: 78
Views: 33,941
I didn't realize that bwa includes its own...
I didn't realize that bwa includes its own solid2fastq.pl...
I've just tried it and seems to work fine: running 'bwa aln' with the fastq file produced in this way does not raises the segmentation...
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Forum: Bioinformatics
02-03-2010, 01:40 AM
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Replies: 78
Views: 33,941
I've tried the solid2fastq C-version of BFAST...
I've tried the solid2fastq C-version of BFAST 0.6.3a. It worked apparently fine, since read names are not truncated as original csfastaToFastq script does. However, using the fastq produced by...
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