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Search: Posts Made By: milo0615
Forum: Bioinformatics 09-01-2016, 04:53 PM
Replies: 1
Views: 1,838
Posted By milo0615
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

**...
Forum: Bioinformatics 03-08-2016, 03:10 PM
Replies: 252
Views: 105,807
Posted By milo0615
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...
Forum: Bioinformatics 03-08-2016, 02:07 PM
Replies: 252
Views: 105,807
Posted By milo0615
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...
Forum: Bioinformatics 03-08-2016, 12:52 PM
Replies: 252
Views: 105,807
Posted By milo0615
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...
Forum: Bioinformatics 03-08-2016, 10:53 AM
Replies: 252
Views: 105,807
Posted By milo0615
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...
Forum: Bioinformatics 01-21-2016, 03:37 PM
Replies: 5
Views: 1,782
Posted By milo0615
hi g36, Which tools did you use for mapping...

hi g36,

Which tools did you use for mapping and SNP discovery?
Forum: Bioinformatics 01-21-2016, 03:20 PM
Replies: 0
Views: 1,074
Posted By milo0615
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...
Forum: Bioinformatics 08-19-2015, 03:25 PM
Replies: 4
Views: 2,072
Posted By milo0615
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 ...
Forum: Bioinformatics 08-18-2015, 01:39 PM
Replies: 4
Views: 2,072
Posted By milo0615
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
Forum: Bioinformatics 08-18-2015, 01:28 PM
Replies: 2
Views: 1,606
Posted By milo0615
Hi JT Guan, Were you able to use PhastCons...

Hi JT Guan,

Were you able to use PhastCons to analyze your data? Please let me know. I am currently analyzing a multiple alignment with three plant species.


Thank you,

-Milo
Forum: Bioinformatics 07-21-2015, 08:41 AM
Replies: 2
Views: 2,829
Posted By milo0615
Hi fahmida, Were you able to figure out what...

Hi fahmida,

Were you able to figure out what is causing that error? I have the same problem. Please let me know.

Thank you,

-Milo
Forum: Bioinformatics 07-13-2015, 03:13 PM
Replies: 27
Views: 39,180
Posted By milo0615
Hi BENM, Did you post the corrected...

Hi BENM,

Did you post the corrected 'calengc.pl' script?
Forum: Bioinformatics 07-10-2015, 03:47 PM
Replies: 7
Views: 2,372
Posted By milo0615
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...
Forum: Bioinformatics 04-17-2015, 01:20 PM
Replies: 10
Views: 2,436
Posted By milo0615
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...
Forum: Bioinformatics 04-17-2015, 11:06 AM
Replies: 10
Views: 2,436
Posted By milo0615
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...
Forum: Bioinformatics 04-16-2015, 05:06 PM
Replies: 10
Views: 2,436
Posted By milo0615
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).
...
Forum: Bioinformatics 04-16-2015, 04:11 PM
Replies: 10
Views: 2,436
Posted By milo0615
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,
Forum: Bioinformatics 04-16-2015, 12:57 PM
Replies: 4
Views: 1,637
Posted By milo0615
Hi Jean, were you able to figure it out?...

Hi Jean,

were you able to figure it out? Please share.
Forum: Bioinformatics 04-16-2015, 12:48 PM
Replies: 10
Views: 2,436
Posted By milo0615
Exclamation 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...
Forum: Bioinformatics 02-26-2015, 11:15 AM
Replies: 20
Views: 10,532
Posted By milo0615
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...
Forum: Bioinformatics 11-11-2014, 01:48 PM
Replies: 0
Views: 1,116
Posted By milo0615
Amos/MuMMer/Minimus2 postnuc running multikmer assembly

Hello,

I am using the following protocol to Merge a multikmer assembly using CDHit && Amos.
protocol: http://ged.msu.edu/angus/metag-assembly-2011/velvet-multik.html

However, after running...
Forum: Bioinformatics 11-02-2014, 12:50 PM
Replies: 2
Views: 3,048
Posted By milo0615
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
...
Forum: Bioinformatics 08-18-2014, 10:58 AM
Replies: 1
Views: 1,860
Posted By milo0615
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...
Forum: Bioinformatics 06-06-2014, 12:30 PM
Replies: 0
Views: 1,498
Posted By milo0615
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...
Forum: Bioinformatics 05-09-2014, 04:02 PM
Replies: 2
Views: 1,858
Posted By milo0615
Hi RyNkA, I am going to use ABySS to do a...

Hi RyNkA,

I am going to use ABySS to do a paired-end assembly of the multiple libraries. Thank you for your reply.
Showing results 1 to 25 of 39

 


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