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Forum: Bioinformatics 01-23-2014, 08:19 AM
Replies: 3
Views: 2,827
Posted By jomaco
Hi, Did you have any luck with this problem?...

Hi,

Did you have any luck with this problem?

I have been experiencing it for some time, but the only way round it seems to be running RepeatModeler many many times until it finally (and...
Forum: Bioinformatics 01-23-2014, 08:15 AM
Replies: 3
Views: 2,827
Posted By jomaco
Hi, Did you have any luck with this problem?...

Hi,

Did you have any luck with this problem?

I have been experiencing it for some time, but the only way round it seems to be running RepeatModeler many many times until it finally (and...
Forum: Bioinformatics 03-19-2013, 01:23 PM
Replies: 1
Views: 1,397
Posted By jomaco
BWA: Should Sai/Sam sequences processed match

Hi,

After running BWA I get an output like this:

[bwa_sai2sam_pe_core] print alignments... 0.66 sec
[bwa_sai2sam_pe_core] 197538574 sequences have been processed.
[main] Version: 0.6.1-r104
...
Forum: Bioinformatics 03-18-2013, 04:54 AM
Replies: 1
Views: 1,182
Posted By jomaco
I was able to plot these files by removing the...

I was able to plot these files by removing the lines starting with "-" and then creating a line graph on Excel.
Forum: Bioinformatics 03-18-2013, 03:44 AM
Replies: 2
Views: 1,323
Posted By jomaco
Thanks. Very useful, I wasn't aware you could...

Thanks. Very useful, I wasn't aware you could combine -F and -f
Forum: Bioinformatics 03-18-2013, 03:28 AM
Replies: 4
Views: 2,631
Posted By jomaco
Did anyone have any luck finding an answer to...

Did anyone have any luck finding an answer to this?

Thanks
Forum: Bioinformatics 03-18-2013, 03:27 AM
Replies: 1
Views: 2,794
Posted By jomaco
DP4 field & VCF parsing/SNP analysis

Hi

In the samtools manual, for the DP4 field it states that the:

"...sum can be smaller than DP because low-quality bases are not counted."

I wonder, what is the cut-off for this? How low...
Forum: Bioinformatics 03-18-2013, 03:26 AM
Replies: 4
Views: 2,631
Posted By jomaco
Did anyone have any luck finding an answer to...

Did anyone have any luck finding an answer to this?

Thanks
Forum: Bioinformatics 03-05-2013, 02:57 AM
Replies: 2
Views: 1,323
Posted By jomaco
Samtools filtering

Hi

I am trying to filter for those reads which are mapped but where the mate is unmapped.

I tried:

bsub "source samtools-0.1.18; samtools view -bt -f 8 F3H.fa.fai L2557F3H.sam >...
Forum: Bioinformatics 02-15-2013, 03:33 AM
Replies: 1
Views: 1,182
Posted By jomaco
ABySS graphs

Hi

ABySS produces .hist files at various points in the assembly. I have been told omnigraphsketcher can be used to plot these files. However, I am using windows and this application only works on...
Forum: Bioinformatics 02-14-2013, 03:50 AM
Replies: 1
Views: 1,460
Posted By jomaco
Whole genome alignment (or the opposite of it?)

Hi

We have two preliminary genome assemblies (which are fragmented libraries of contigs/scaffolds comprising sequencing data from two different types of the same species of plant). We believe the...
Forum: Bioinformatics 02-05-2013, 08:32 AM
Replies: 8
Views: 4,395
Posted By jomaco
I think I have finally solved the problem. The...

I think I have finally solved the problem. The reference sequences I was aligning to are upregulated transcripts derived from transcriptome data. The output files from trinity had a format such as...
Forum: Bioinformatics 02-05-2013, 02:14 AM
Replies: 8
Views: 4,395
Posted By jomaco
Hi Thanks for your reply. I ran the...

Hi

Thanks for your reply. I ran the following set of commands to get to this point:

source bwa-0.6.1;

bwa index -a is upregoakextractreal.fa

bsub -o saiout1 -n 8 -R "rusage[mem=40000]...
Forum: Bioinformatics 02-04-2013, 10:01 AM
Replies: 8
Views: 4,395
Posted By jomaco
BWA Sampe error - [bns_restore_core] fail to open file '1888]

Hi

I ran bwa aln and it completed successfully. I have tried it numerous times and the same file sizes result so I assume this step is working correctly and the files are not truncated. However,...
Forum: Bioinformatics 01-28-2013, 03:56 AM
Replies: 0
Views: 1,094
Posted By jomaco
SNP calling problems

Hi

I am carrying out alignments using BWA and Bowtie and then using samtools to produce some fairly large SAM files (>100G) followed by calling SNPs and producing VCF files.

I have found that...
Forum: Bioinformatics 01-31-2012, 06:24 AM
Replies: 1
Views: 3,069
Posted By jomaco
Standalone Blast output

Hi

When looking at the output from standalone blast I see this:

<Hsp_hit-from>76056</Hsp_hit-from>
<Hsp_hit-to>76901</Hsp_hit-to>
...
Forum: Bioinformatics 01-26-2012, 11:12 AM
Replies: 0
Views: 1,596
Posted By jomaco
Statistics after mapping

Hi

I have mapped RNAs to the genome sequence I am working on. Following this I estimated the percentage of the genome that is repetitive and I have used this is to infer the number of RNAs that...
Forum: Bioinformatics 11-26-2011, 07:02 AM
Replies: 3
Views: 3,268
Posted By jomaco
Hi Thanks for your replies. I was using...

Hi

Thanks for your replies.

I was using makeblastdb which I think formats the db so I think my problem was a permissions issue. I ran tblastn from a folder in my documents and the output file...
Forum: Bioinformatics 11-21-2011, 05:43 PM
Replies: 3
Views: 3,268
Posted By jomaco
Standalone blast

Hi

I have downloaded standalone blast and formatted a nucleotide database. I wish to use tblastn to compare Arabidopsis proteins against it. I made a db folder in the folder where blast is saved...
Forum: Bioinformatics 10-30-2011, 07:41 AM
Replies: 6
Views: 4,097
Posted By jomaco
Sorry. You're right it does. Someone who asked me...

Sorry. You're right it does. Someone who asked me to run the alignment told me it was required to convert the read file to fastaq format. Perhaps I should not be so trustful next time!

I have now...
Forum: Bioinformatics 10-30-2011, 06:13 AM
Replies: 9
Views: 3,138
Posted By jomaco
It was indeed a memory problem. Top showed that...

It was indeed a memory problem. Top showed that memory usage climbed up to 80% with 100% CPU usage. I accessed /var/log/kern.log which reported '...ubuntu kernel: [19459.333979] Out of memory: Kill...
Forum: Bioinformatics 10-30-2011, 06:09 AM
Replies: 6
Views: 4,097
Posted By jomaco
Convert FASTA to FASTAQ

Hi

I need to map small RNA sequences onto a genome using BWA.

The read file (reads.fa) is in the following format:

>EMUNAOL01D19UY length 23 duplications 0
CGTCTTGGTTTGTCTAAAGGGGC...
Forum: Bioinformatics 10-24-2011, 02:19 AM
Replies: 9
Views: 3,138
Posted By jomaco
Hi. 'petunia.fa' is the whole petunia genome and...

Hi. 'petunia.fa' is the whole petunia genome and is a 1.3GB file. When you a say a lot of memory, how much do you mean? I am trying this on a PC running ubuntu with 4GB RAM. Would it be useful to try...
Forum: Bioinformatics 10-23-2011, 04:49 PM
Replies: 9
Views: 3,138
Posted By jomaco
Thanks for your help again but I couldn't see...

Thanks for your help again but I couldn't see that I missed anything. I tried the '>' idea too but no luck. I tried to configure the program again and when this didn't work I thought it might a good...
Forum: Bioinformatics 10-21-2011, 03:52 PM
Replies: 9
Views: 3,138
Posted By jomaco
That's great thanks! Worked perfectly. I can now...

That's great thanks! Worked perfectly. I can now run the RepeatMasker command. Unfortunately, however, I now have a new problem. I typed the command:

RepeatMasker -species petunia petunia.fa
...
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