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Search: Posts Made By: javijevi
Forum: Bioinformatics 05-13-2014, 09:05 AM
Replies: 1
Views: 5,413
Posted By javijevi
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
...
Forum: Bioinformatics 03-10-2010, 08:34 AM
Replies: 42
Views: 110,081
Posted By javijevi
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?
Forum: Bioinformatics 03-10-2010, 05:33 AM
Replies: 42
Views: 110,081
Posted By javijevi
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...
Forum: Bioinformatics 02-25-2010, 10:40 AM
Replies: 78
Views: 32,447
Posted By javijevi
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...
Forum: RNA Sequencing 02-23-2010, 02:01 AM
Replies: 21
Views: 18,873
Posted By javijevi
Thanks a lot. I'll give a try... if I manage to...

Thanks a lot. I'll give a try... if I manage to understand it...



Yes. Learning C is my first TODO.



None in my case. I just wanted to get rid of duplicated reads from the very...
Forum: RNA Sequencing 02-22-2010, 07:04 AM
Replies: 21
Views: 18,873
Posted By javijevi
I see. My script does the same, but I think it is...

I see. My script does the same, but I think it is impractical for hugue datasets. For example, with a 43 GB SAM file (corresponding to the mapping of a 33 GB fastq file), I guess that I need at least...
Forum: RNA Sequencing 02-22-2010, 05:04 AM
Replies: 21
Views: 18,873
Posted By javijevi
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,...
Forum: RNA Sequencing 02-18-2010, 10:25 AM
Replies: 21
Views: 18,873
Posted By javijevi
Is there any tool to remove exact duplicate...

Is there any tool to remove exact duplicate reads? It should remove all the reads with the same exact sequence, leaving alone the one with better quality values, shouldn't?
Forum: Bioinformatics 02-16-2010, 09:45 AM
Replies: 7
Views: 4,403
Posted By javijevi
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).
...
Forum: Bioinformatics 02-16-2010, 07:59 AM
Replies: 7
Views: 4,403
Posted By javijevi
Converting nucleotide-space to color-space

Does anybody know where could I find a tool to convert a nucleotide-space sequence to a color-space sequence?

Thanks a lot in advance,
Forum: Bioinformatics 02-13-2010, 04:06 PM
Replies: 78
Views: 32,447
Posted By javijevi
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...
Forum: Bioinformatics 02-10-2010, 09:16 AM
Replies: 21
Views: 6,035
Posted By javijevi
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....
Forum: Bioinformatics 02-10-2010, 07:39 AM
Replies: 21
Views: 6,035
Posted By javijevi
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...
Forum: Bioinformatics 02-10-2010, 06:44 AM
Replies: 78
Views: 32,447
Posted By javijevi
At least not correct enough for bwa pipeline, it...

At least not correct enough for bwa pipeline, it seems. If you have the corresponding FASTA and QUAL files, you can try some script to producing fastq files from them. In the case of SOLiD data, the...
Forum: Bioinformatics 02-10-2010, 06:33 AM
Replies: 21
Views: 6,035
Posted By javijevi
Strange memory corruption error in BFAST match step

Hi, I have a set of 300 million 50-bp long SOLiD reads, and I would like to use BFAST to map them to a reference genome. I've successfully created the color-space reference genome .brfg file, and the...
Forum: Bioinformatics 02-10-2010, 04:40 AM
Replies: 78
Views: 32,447
Posted By javijevi
As far as I know, if you use fastq files the...

As far as I know, if you use fastq files the problem is the same: you've got a wrong fastq file.
Forum: Bioinformatics 02-09-2010, 02:43 PM
Replies: 5
Views: 1,889
Posted By javijevi
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...
Forum: Bioinformatics 02-09-2010, 10:57 AM
Replies: 5
Views: 1,889
Posted By javijevi
Just to tell that I made a mistake in copying...

Just to tell that I made a mistake in copying twice the last two lines of the output.
Forum: Bioinformatics 02-09-2010, 10:54 AM
Replies: 5
Views: 1,889
Posted By javijevi
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...
Forum: Bioinformatics 02-08-2010, 05:43 AM
Replies: 9
Views: 6,746
Posted By javijevi
Oops... I feel my ears growing like a donkey......

Oops... I feel my ears growing like a donkey... My poor english... I misunderstood 'power of two'. I thought it was 'multiple of two'. I strongly apologize.
Forum: Bioinformatics 02-08-2010, 03:47 AM
Replies: 78
Views: 32,447
Posted By javijevi
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...
Forum: Bioinformatics 02-08-2010, 03:30 AM
Replies: 9
Views: 6,746
Posted By javijevi
I used -n 6 (my box has 8 cores, but I wanted to...

I used -n 6 (my box has 8 cores, but I wanted to have 2 of them free), and also get an error indicating that number of thread must be a power of two. Why do you propose 4 or 8 threads in the previous...
Forum: Bioinformatics 02-05-2010, 03:52 PM
Replies: 78
Views: 32,447
Posted By javijevi
I'm sorry for the previous message. It is not...

I'm sorry for the previous message. It is not true. The fastq file produced by the solid2fastq.pl script shipped with bwa distribution also causes segmentation fault error in my computer.
Forum: Bioinformatics 02-05-2010, 07:21 AM
Replies: 78
Views: 32,447
Posted By javijevi
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...
Forum: Bioinformatics 02-03-2010, 02:40 AM
Replies: 78
Views: 32,447
Posted By javijevi
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...
Showing results 1 to 25 of 38

 


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