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Search: Posts Made By: gwilymh
Forum: Bioinformatics 10-11-2016, 01:12 PM
Replies: 0
Views: 1,646
Posted By gwilymh
Read depth differs between bcftools and bam-readcount

We are analyzing bam files using bam-readcount and bcftools + mpileup, and comparing the reported level of coverage at specific sites in the genome. We compared both raw read coverage depth and the...
Forum: Bioinformatics 03-30-2016, 01:29 PM
Replies: 0
Views: 1,119
Posted By gwilymh
Samtools is failing to phase bam files accurately

My colleagues and I are assembling transcriptomes from RNASeq data. Our pipeline can (loosely) be outlined as follows:
1. De novo assembly using all RNASeq read data
2. Identification of potential...
Forum: Bioinformatics 03-30-2016, 12:31 PM
Replies: 1
Views: 934
Posted By gwilymh
What type of phred quality scores does samtools 1.3 expect

I am working with NG sequence data that was generated in 2012 using the Illumina HiSeq 1000. I have had some trouble getting samtools to accurately identify heterozygotes and phase bam files...
Forum: Bioinformatics 02-19-2016, 01:19 PM
Replies: 1
Views: 2,041
Posted By gwilymh
Update: One of the sys administrators installed...

Update: One of the sys administrators installed the module for 'application/perl/5.14.4' (the only perl version installed on the cluster). The rnammer now produces a different error. Command:...
Forum: Bioinformatics 02-19-2016, 11:21 AM
Replies: 1
Views: 2,041
Posted By gwilymh
Installation of rnammer-1.2 for Trinnoate: which version Perl XML/Simple.pm is requir

Hi Trinity community,

I am working on step 6. Running RNAMMER to identify rRNA transcripts of the Trinoate protocol detailed on https://trinotate.github.io/ . Getting rnammer to work properly has...
Forum: Bioinformatics 09-18-2015, 01:42 PM
Replies: 1
Views: 963
Posted By gwilymh
A good answer to my questions is given here: ...

A good answer to my questions is given here:
https://groups.google.com/forum/#!topic/trans-abyss/_mHXGbtcO_U

MPI allows multi-threading between nodes in a cluster, while standard multi-threading...
Forum: Bioinformatics 09-17-2015, 03:05 PM
Replies: 2
Views: 2,095
Posted By gwilymh
Problem with SSPACE, multi-threading and memory restrictions

Hi,
I am attempting to use SSPACE version 3 to re-scaffold some mRNA contigs using paired-end RNA-Seq data. While SSPACe was designed for rescaffolding genomes, I see no reason why it should not...
Forum: Bioinformatics 09-05-2015, 03:54 PM
Replies: 0
Views: 1,328
Posted By gwilymh
Trinity 2.0.6 jellyfish compilation error - error: ‚all_of‚ is not a member of ‚std‚

I am trying to install trinity v2.0.6 on a Linux cluster, and am getting a strange error message after running ./configure and then make:

make[1]: Entering directory...
Forum: Bioinformatics 06-03-2015, 08:26 AM
Replies: 1
Views: 963
Posted By gwilymh
MPI and multi-threading in trans-abyss

Can anyone explain to me the difference between MPI processes and multithreading in trans-abyss?

Are the two mutually exclusive alternative forms of parallel processing? (The literature...
Forum: Bioinformatics 05-26-2015, 04:27 PM
Replies: 1
Views: 1,554
Posted By gwilymh
The following code worked. I dropped the unpaired...

The following code worked. I dropped the unpaired reads.

transabyss --se $INPUT_F $INPUT_R --pe $INPUT_F $INPUT_R --outdir $WORKING_DIR --name $OUTPUT_FILE --threads 10 --mpi 10 --indel 4
Forum: Bioinformatics 05-13-2015, 01:56 PM
Replies: 0
Views: 1,636
Posted By gwilymh
How best to use --bflyHeapSpaceMax and --bflyGCThreads on Trinity

I am currently using trinity v2.6.0. My jobs keep crashing at the butterfly stage of the analysis, with such error messages as:
succeeded(1008), failed(108076) 99.9771% completed. Invalid...
Forum: Bioinformatics 02-18-2015, 01:57 PM
Replies: 3
Views: 3,208
Posted By gwilymh
Problem using the Trinity script align_and_estimate_abundance.pl with RSEM

Hi,
I have assembled RNA-Seq data do novo in Trinity, and am now trying to estimate the abundance of the transcripts that were identified. I used TopHat to align the RNA-Seq fastq reads against the...
Forum: Bioinformatics 02-07-2015, 09:57 AM
Replies: 1
Views: 1,554
Posted By gwilymh
What is the specific syntax needed for Trans-ABySS to analyze both SE and PE files?

I have been trying for days to get Trans-ABySS to run a set of paired-end and single-end fastq files. The paired in data is stored in two files, one with the forward reads and the other with the...
Forum: Bioinformatics 02-03-2015, 10:06 AM
Replies: 0
Views: 1,686
Posted By gwilymh
Cuffmerge outputs only exon annotation data

Hi,

I am analyzing RNA-Seq data to discover new genes, exons and polymorphic sites. I recently aligned the RNA of 7 different tissue samples against a reference genome using TopHat, and cleaned up...
Forum: RNA Sequencing 01-06-2015, 02:41 PM
Replies: 3
Views: 2,045
Posted By gwilymh
What do you mean specifically when you say...

What do you mean specifically when you say 'sorting'?
Forum: RNA Sequencing 11-26-2014, 04:37 PM
Replies: 0
Views: 1,858
Posted By gwilymh
Improve accuracy of trinity RNA-Seq assemblies with --min_glue and/or --min_kmer_cov

Hi,
Does anyone know if it possible to improve the accuracy of Trinity RNA-Seq assemblies using --min_glue and/or --min_kmer_cov flags?

The trinity manual suggests raising the --min_kmer_cov...
Forum: Bioinformatics 11-17-2014, 05:01 PM
Replies: 1
Views: 1,853
Posted By gwilymh
GATK RNA-Seq pathway Split 'n' Trim- problems with .bai and .fai index compatibility

I am processing aligned RNA-Seq data to get phased haplotypes of novel genes in sea stars. I am working through the analysis pipeline that used the Genome Analysis Toolkit suite of software, and is...
Forum: Bioinformatics 10-16-2014, 08:38 AM
Replies: 0
Views: 1,459
Posted By gwilymh
Interpretation of bwa output - has it used all the reads

I am analyzing an RNASeq data set. I have screened reads in Trimmomatic and aligned them using bwa mem. The reads are mostly 100bp long, but a minority are as short as 30bp. Reads are submitted in...
Forum: Bioinformatics 10-06-2014, 03:22 PM
Replies: 4
Views: 2,454
Posted By gwilymh
Thank you all for the responses. Where can one...

Thank you all for the responses. Where can one find the documentation for the butterfly-specific (--bfly*) options? There does not seem to be any in the Trinity manual, webpage or --help...
Forum: Bioinformatics 09-24-2014, 03:19 PM
Replies: 4
Views: 2,454
Posted By gwilymh
Trinity error around number of CPU's and Java virtual machine

Hi,

I have been sending trinity jobs to a cluster under differing conditions. If I request 1 node with one or two processes (CPU's) and 2GB of memory for each process/CPU, the program runs without...
Forum: Bioinformatics 08-04-2014, 03:36 PM
Replies: 1
Views: 848
Posted By gwilymh
What exactly are "read groups"

I am reading the samtools manual. For the -r and -R flags in the view function, the manual refers to "read groups". I have not been able to work out exactly what read groups are. Can anyone enlighten...
Forum: Bioinformatics 07-18-2014, 08:13 PM
Replies: 10
Views: 5,357
Posted By gwilymh
Thank you blakeoft. I dropped the PE flag and...

Thank you blakeoft. I dropped the PE flag and added individual file names for each output file and the program executed properly.

NB: I also tried using the -baseout <outputBase> flag rather than...
Forum: Bioinformatics 07-18-2014, 09:36 AM
Replies: 10
Views: 5,357
Posted By gwilymh
Problem with Trimmomatic: will not acknowledge commands

I am trying to use the program Trimmomatic to removed adapter sequences from an Illumina paired-end read over a computer cluster. While I can get the program to open, it will either not acknowledge...
Forum: Bioinformatics 03-10-2014, 08:46 AM
Replies: 1
Views: 1,120
Posted By gwilymh
Cuffdiff thread option

Can anyone explain to me the following option in CuffDiff:


-p/--num-threads <int>
Use this many threads to align reads. The default is 1.

What are threads? Will it take longer to run the...
Forum: Bioinformatics 03-10-2014, 08:43 AM
Replies: 1
Views: 1,167
Posted By gwilymh
Can CuffDiff runs be resumed if they are interrupted?

Can pipelines running cufflinks or cuffdiff be resumed if they are interrupted? Or do they always have to be restarted from the beginning?
Showing results 1 to 25 of 72

 


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