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Search: Posts Made By: alig
Forum: Bioinformatics 04-01-2015, 07:06 PM
Replies: 0
Views: 2,738
Posted By alig
CoNIFER index 0 is out of bounds for axis 0 with size 0

Hi,

I am having issues with Conifer plotting the call images.

It manages for about half the chromosomes - chr 1, 2, 10 to 19 with this command

python conifer.py plotcalls --input...
Forum: Bioinformatics 10-16-2013, 02:54 PM
Replies: 191
Views: 76,140
Posted By alig
Hello, I've used Tophat 2.0.9 & then HTseq...

Hello,

I've used Tophat 2.0.9 & then HTseq version 0.5.4p3 & just with 3 of my 28 SAM files I get this error.

Error occured in line 63841485 of file RNA8_sorted.sam.
Error: ("'seq' and...
Forum: Bioinformatics 09-09-2013, 06:25 PM
Replies: 191
Views: 76,140
Posted By alig
Hi, I'm having the same issue with one of my...

Hi,
I'm having the same issue with one of my SAM files when using htseq-count.
For some reason, one of my SAM files raises the error:

Error occured in line 38586430 of file RNA7_sorted.sam....
Forum: Bioinformatics 12-16-2012, 02:00 PM
Replies: 8
Views: 5,838
Posted By alig
BWA0.6.2 indexes

Thank you for the information re the new BWA indexes,

All seems to be running now, think my problem was an error in my script.

alig
Forum: Bioinformatics 12-12-2012, 05:55 PM
Replies: 8
Views: 5,838
Posted By alig
bwa_sai2sam_pe fail to locate the index

Hi,

I'm trying to run BWA.0.6.2 I notice that when I index my reference file it is missing some indexes. This seems to be fine if I align single end sequence.

However when I want to run...
Forum: Bioinformatics 06-06-2012, 05:07 PM
Replies: 5
Views: 2,626
Posted By alig
Was this problem ever solved? I have converted...

Was this problem ever solved? I have converted solexa reads using Maq sol2sanger & it adds an extra quality to each read. So then of course Mosaik complains that no. of qualities (66) do not match...
Forum: Bioinformatics 11-17-2011, 08:17 PM
Replies: 21
Views: 5,393
Posted By alig
Bfast Malloc memory error

Hi,

I tried with a hugely smaller dataset & didn't get the error. So then I tried with a different fastq file which I had run through a script to remove any entries which look broken and also had...
Forum: Bioinformatics 11-13-2011, 07:18 PM
Replies: 21
Views: 5,393
Posted By alig
Bfast Malloc memory error

Hi,
Has there been a solution to the Malloc memory error when running Bfast?

I am having the same problem when trying to run bfast bwaaln

bfast+bwa-0.7.0a/bfast/bfast bwaaln -n 0.04 -o 1 -e -1...
Forum: SOLiD 09-29-2011, 06:30 PM
Replies: 9
Views: 7,969
Posted By alig
Parse error at line x, sequence and quality are inconsistent

Hi,

Error as follows:

[samopen] SAM header is present: 84 sequences.
Parse error at line 86: sequence and quality are inconsistent

There have been a few people coming across this error when...
Forum: Bioinformatics 07-01-2011, 12:08 AM
Replies: 0
Views: 1,337
Posted By alig
trouble getting Bowtie aligner to run

Hi,

This is my first time in years I have tried to run Bowtie aligner. I have indexed the reference sequence for colorspace. Now I am trying to align my SOLiD paired end reads. But the program...
Forum: Bioinformatics 06-23-2011, 11:46 PM
Replies: 3
Views: 4,212
Posted By alig
Unhappy BWA align SOLiD PE data gives poor mapping & 0.5% properly paired

Hi,

This is my first attempt at aligning SOLiD paired end sequence which is whole exome data.
F3 file has reads minlength=50, F5-BC file has reads minlength=35

Previously I have only worked...
Forum: Bioinformatics 02-02-2011, 03:19 PM
Replies: 78
Views: 45,112
Posted By alig
breaking contig in gap5

Hi,

Okay, I can't seem to successfully break a contig in gap5, & I cannot open my .aux file in gap4 to break a contig and search for unpadded positions.

I tried to break a contig in gap5 by...
Forum: Bioinformatics 02-02-2011, 12:46 PM
Replies: 78
Views: 45,112
Posted By alig
Searching unpadded position in Gap5

Hi James,

That's a shame, but I imagine it's not an easy task.

Unfortunately my contig is the length of the X chromosome. But I am only interested in a small interval at the beginning so I'll...
Forum: Bioinformatics 01-30-2011, 07:14 PM
Replies: 78
Views: 45,112
Posted By alig
how search for unpadded positions in gap5

Hi,

I would like to search for unpadded positions in gap5 as none of my variant positions match up in gap5 as the search position box within edit contig view includes pads.

How do I search for...
Forum: Bioinformatics 01-20-2011, 05:42 PM
Replies: 78
Views: 45,112
Posted By alig
Smile installing gap5

Hi,
Thank you for pointing me in all the right directions. I got confused and did make install after configure.
All good now, looking forward to using gap5
cheers alig
Forum: Bioinformatics 01-19-2011, 04:55 PM
Replies: 78
Views: 45,112
Posted By alig
tk_utils Error when make gap5

Hi James,

Thank you for your quick response. I installed the dev package for staden io_lib using synaptic package manager. I now have a different error.

make install
mkdir -p...
Forum: Bioinformatics 01-16-2011, 08:23 PM
Replies: 78
Views: 45,112
Posted By alig
Unhappy tk_utils Error when make gap5

Hi,

I still cannot launch gap5 & really w:(ant to get on & use the program to view my Next Gen data.

When I type ./gap5 to launch it I still get
couldn't read file...
Forum: Bioinformatics 12-02-2010, 04:12 PM
Replies: 21
Views: 33,819
Posted By alig
fq_all2std

Hi,

the "std2qual" is part of the perl script "fq_all2std.pl" which comes with maq-0.7.1

thanks

ali
Forum: Bioinformatics 09-30-2010, 10:24 PM
Replies: 78
Views: 45,112
Posted By alig
Unhappy problems lauching gap5 and installing manual

Hi,
sorry me again.
I get the following message when try to launch gap5
couldn't read file "/home/neuro/Documents/Gap5/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or...
Forum: Bioinformatics 09-30-2010, 04:25 PM
Replies: 78
Views: 45,112
Posted By alig
Smile Re: no functioning samtools when configuring gap5

Hi James,

Thank you very much for your quick reply. I had an earlier version of samtools which didn't have a Makefile to edit.
After downloading samtools-0.1.8 & editing the Makefile by adding...
Forum: Bioinformatics 09-29-2010, 04:40 PM
Replies: 78
Views: 45,112
Posted By alig
Red face No functioning samtools found

Hello,

Is anyone else getting this error when configuring Gap5?

configure: WARNING: No functioning samtools found
configure: WARNING: Gap5/tg_index will have reduced functionality

I've got...
Forum: Bioinformatics 06-09-2010, 07:39 PM
Replies: 20
Views: 5,325
Posted By alig
Probs trying to run variationhunter

Hi john,

I forgot to say that I'd put the path to the program executables in my bash shell. They all reside in the same directory. So when I echo $PATH
...
Forum: Bioinformatics 06-09-2010, 06:23 PM
Replies: 20
Views: 5,325
Posted By alig
Unhappy Problem trying to run VariationHunter

Hi,

I'm just trying to run the program VariationHunter, but I get the following error.

There doesn't seem to be any instructions for install & make just returns
make: Nothing to be done for...
Forum: Bioinformatics 08-12-2009, 07:02 PM
Replies: 3
Views: 2,182
Posted By alig
Tophat errors

Hi,

I have just run Tophat for the first time and get the following errors.

It still gives me some output files, but I would like to be sure that it did run properly before continuing with the...
Forum: Bioinformatics 06-17-2009, 08:56 PM
Replies: 78
Views: 45,112
Posted By alig
gap5 aborts

Hi,

I ran tg_index on a Consed ace file assembly of illumina reads & it appeared to work without any errors.

But when I open the converted gap5.aux file there is just the Refseq sequence in the...
Showing results 1 to 25 of 43

 


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