Forum: Bioinformatics
09-01-2016, 05:53 PM
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Replies: 1
Views: 1,899
MAKER Exonerate Error
Hello,
I am currently running MAKER version 2.31.8 using MPI but I keep getting the following error when running Exonerate:
Maker command used: mpiexec -mca btl ^openib -n 16 maker
**...
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Forum: Bioinformatics
03-08-2016, 04:10 PM
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Replies: 252
Views: 107,847
Hi sunnycqcn,
My libraries.txt file looks...
Hi sunnycqcn,
My libraries.txt file looks like the following:
gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
gjGA bowtie GerJamesonii_1_P.fastq...
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Forum: Bioinformatics
03-08-2016, 03:07 PM
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Replies: 252
Views: 107,847
Hi fahmida,
If I use -x = 0 the assembly...
Hi fahmida,
If I use -x = 0 the assembly stats such as the N50, n>200, and max length stay the same. I have already emailed the SSPACE developers for an older version of it.
Thank you for your...
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Forum: Bioinformatics
03-08-2016, 01:52 PM
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Replies: 252
Views: 107,847
Hi sunnycqcn,
The command I used is as...
Hi sunnycqcn,
The command I used is as follows. Thank you for your help
>perl $HOME/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s...
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Forum: Bioinformatics
03-08-2016, 11:53 AM
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Replies: 252
Views: 107,847
Hello,
Were you guys able to figure it out?...
Hello,
Were you guys able to figure it out? I am running SSPACE x_64 with options (x=1 and T=16) but I am getting the following error:
=>Mon Mar 7 15:46:00 2016: Extending of contigs with...
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Forum: Bioinformatics
01-21-2016, 04:37 PM
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Replies: 5
Views: 1,837
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Forum: Bioinformatics
01-21-2016, 04:20 PM
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Replies: 0
Views: 1,112
SNP Discovery From De Novo Assembly
Hello,
I have Illumina pair-end reads of two species. Major objective is to identify SNP among both the species. I did the de novo assembly of species 1 and 2 using ABYSS, then compared the two...
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Forum: Bioinformatics
08-19-2015, 04:25 PM
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Replies: 4
Views: 2,169
Hi koustavpal,
Thank you for the quick...
Hi koustavpal,
Thank you for the quick reply. I am currently aligning two de novo plant genomes (wild and domesticated genomes) and I am using a related plant genome as reference. My goal is to ...
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Forum: Bioinformatics
08-18-2015, 02:39 PM
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Replies: 4
Views: 2,169
Hi koustavpal,
Were you able to figure it...
Hi koustavpal,
Were you able to figure it out? What was causing the problem? what Phastcons command did you use? I am in the same situation. Please let me know.
thank you,
-Milo
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Forum: Bioinformatics
08-18-2015, 02:28 PM
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Replies: 2
Views: 1,672
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Forum: Bioinformatics
07-21-2015, 09:41 AM
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Replies: 2
Views: 3,014
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Forum: Bioinformatics
07-13-2015, 04:13 PM
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Replies: 27
Views: 39,895
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Forum: Bioinformatics
07-10-2015, 04:47 PM
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Replies: 7
Views: 2,435
Hi abysslover,
Were you able to align the...
Hi abysslover,
Were you able to align the genomes against each other? I currently have two plant de novo assemblies generated by Abyss and a reference genome from a closed related specie. I would...
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Forum: Bioinformatics
04-17-2015, 02:20 PM
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Replies: 10
Views: 2,596
Hi GenoMax,
I did use Mauve. Attached is a...
Hi GenoMax,
I did use Mauve. Attached is a pdf with the Mauve results of largest 10 contigs for both assemblies (gerbera_alignment.pdf). However, Mauve does not work when I align the largest 10...
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Forum: Bioinformatics
04-17-2015, 12:06 PM
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Replies: 10
Views: 2,596
Hi GenoMax,
I took the longest 10 contigs...
Hi GenoMax,
I took the longest 10 contigs from each assembly (>8500 bp with a max length of 120 K for assembly 1 and 104 K for assembly 2) and BLAT aligned them together. They seem to be pretty...
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Forum: Bioinformatics
04-16-2015, 06:06 PM
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Replies: 10
Views: 2,596
Hi GenoMax,
I do no have a related reference...
Hi GenoMax,
I do no have a related reference genome. Therefore, I aligned both assemblies against each other. My specie is a diploid plant with a 2C DNA value estimated at 5.1 pg (about 5.0 Gb).
...
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Forum: Bioinformatics
04-16-2015, 05:11 PM
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Replies: 10
Views: 2,596
Hi GenoMax,
Thank you for replying.
...
Hi GenoMax,
Thank you for replying.
Assembly a is 444.5MB and it contains 1.4M contigs
Assembly b is 526.1MB and it contains 1.6M contigs
Please advice.
Thank you,
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Forum: Bioinformatics
04-16-2015, 01:57 PM
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Replies: 4
Views: 1,723
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Forum: Bioinformatics
04-16-2015, 01:48 PM
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Replies: 10
Views: 2,596
Comparative Genomics - BLAT
Hello,
I have assembled two related species using Abyss. However, I would like to know if there is a significant difference between the two genomes. A way of doing this is by aligning both...
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Forum: Bioinformatics
02-26-2015, 12:15 PM
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Replies: 20
Views: 10,688
Hi kbushley,
I am also trying to merge six...
Hi kbushley,
I am also trying to merge six different k-mer assemblies from Abyss. Were you able to merge yours? Can you share the program the guy from your department wrote? Please let me know. I...
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Forum: Bioinformatics
11-11-2014, 02:48 PM
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Replies: 0
Views: 1,189
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Forum: Bioinformatics
11-02-2014, 01:50 PM
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Replies: 2
Views: 3,115
toAmos error
Hi SLB,
Were you able to figure it out? I am having the same error trying to combine abyss output. I am following this protocol: http://ged.msu.edu/angus/metag-assembly-2011/velvet-multik.html
...
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Forum: Bioinformatics
08-18-2014, 11:58 AM
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Replies: 1
Views: 1,926
SOAPDenovo-Trans Error - Abored (Core Dumped)
Hello,
I am trying to de novo assemble a small SOLiD file with SOAPDenovo-Trans but I get the following error:
./SOAPdenovo-Trans-31kmer all -K 31 -p 8 -s config -o Diplomat
The version...
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Forum: Bioinformatics
06-06-2014, 01:30 PM
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Replies: 0
Views: 1,555
abyss-pe Read File Error:
Hello,
I am trying to run abyss-pe but I get the following error:
0: Reading `../../GerRegGA/GerRegina_1_trimmed.fastq'...
1: Reading `../../GerRegGA/GerRegina_2_trimmed.fastq'...
2: Reading...
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Forum: Bioinformatics
05-09-2014, 05:02 PM
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Replies: 2
Views: 1,927
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