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Forum: Bioinformatics 08-25-2013, 07:25 PM
Replies: 0
Views: 1,645
Posted By will.jackson
Problems with CEGMA dependency installation

Hi everyone,
I am having trouble installing wise2.2.3-rc7 for running CEGMA. This is the version that the authors of CEGMA recommend but I run into the following error when I run $make all


(cd...
Forum: Bioinformatics 02-27-2013, 05:19 PM
Replies: 3
Views: 2,676
Posted By will.jackson
Hi lorendarith, Thanks for the quick reply. I...

Hi lorendarith,
Thanks for the quick reply. I am working on a diploid genome and have a polymorphism rate of 1/118, so HAPLOIDIFY looks like a good option. Could you explain a little further what...
Forum: Bioinformatics 02-27-2013, 03:39 PM
Replies: 3
Views: 2,676
Posted By will.jackson
Haploidify in ALLPATHS-LG

Hi,
Could someone please explain to me what the HAPLOIDIFY function does in ALLPATHS-LG? I have done two assemblies with ALLPATHS-LG - one with HAPLOIDIFY on and one with it off. The resulting...
Forum: Bioinformatics 02-26-2013, 07:14 PM
Replies: 0
Views: 1,395
Posted By will.jackson
Contig coverage from ALLPATHS-LG

Hi,
I have recently done my first de novo assembly with ALLPATHS-LG. I was wondering if it was possible to determine the coverage for each of the contigs generated in the assembly? I found the...
Forum: Sample Prep / Library Generation 01-20-2013, 06:15 PM
Replies: 0
Views: 2,228
Posted By will.jackson
Does DAPI or Hoechst stains interfere with PCR or NGS?

Hi everyone,
I would like to isolate some nuclei from some dikaryotic cells (2 nuclei per cell) and would like to use DAPI or Hoechst stain to label the nuclei. Does anyone know if these stains will...
Forum: Bioinformatics 11-05-2012, 01:06 PM
Replies: 10
Views: 4,314
Posted By will.jackson
Hi, Thanks for your reply Pablo, I tried doing...

Hi,
Thanks for your reply Pablo, I tried doing what you said and I broke down my files and kept getting the segfault even when the file was only 100 lines long(!). I think maybe I have a lot of...
Forum: Bioinformatics 11-04-2012, 04:12 PM
Replies: 1
Views: 960
Posted By will.jackson
Silly error

Hi,
After thinking about my how I loaded up the sequences over the weekend, I realised I had made a really silly mistake and loaded the reads in pairs and not comma delimited left reads then comma...
Forum: Bioinformatics 10-31-2012, 02:18 PM
Replies: 1
Views: 960
Posted By will.jackson
Is there a maximum number of reads able to be loaded into tophat

Hi everyone,
I am currently mapping some RNAseq reads back to a reference genome I have generated. I did a test run the other day with half of my data (three biological replicates of one cell type)...
Forum: Bioinformatics 10-31-2012, 01:58 PM
Replies: 10
Views: 4,314
Posted By will.jackson
I have had the same problem with the filtering...

I have had the same problem with the filtering parameters of gffread (-J, -V -H etc). Can anyone suggest another program that does a similar thing to gffread? That is, filter transcripts based on CDS...
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