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Question: mapping NGS data with BWA for Illumina
0
gravatar for margherita.c86
3.8 years ago by
margherita.c86 • 0
France
margherita.c86 • 0 wrote:

Hello!

 

i am trying to map single-end reads using BWA for Illumina but an error accoured:

Error aligning sequence. Saw ASCII character 35 but expected 64-based Phred qual.
Try not specifying --solexa1.3-quals/--phred64-quals.
terminate called after throwing an instance of 'int'
/bin/sh: line 1: 16919 Aborted                 (core dumped) bowtie -q -p 6 -S --phred64-quals /galaxy-repl/main/scratch/tmpR0OlN2/tmpF3FcS4 /galaxy-repl/main/files/010/302/dataset_10302796.dat > /galaxy-repl/main/files/010/302/dataset_10302797.dat

does somebody know how to fix it?

 

thank you in advance

Margherita

 
bwa • 1.2k views
ADD COMMENT • link •
modified 3.8 years ago by Bjoern Gruening ♦ 5.1k • written 3.8 years ago by margherita.c86 • 0
1
gravatar for Bjoern Gruening
3.8 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

seems you have an old FASTQ format. Have a look at the "FASTQ Groomer convert between various FASTQ quality formats" tool and convert your file before you map them.

Ciao,

Bjoern
ADD COMMENT • link modified 3.8 years ago • written 3.8 years ago by Bjoern Gruening ♦ 5.1k

I am just going to add a link in here to some help for determining the datatype (and associated quality score scaling). May help when determining the appropriate settings when grooming. Thanks! Jen, Galaxy team

http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

thank you !

i worked but now i am blocked with the IGV visualitation of the data mapped... i did a conversione SAM to BAM but IGV doesn't recognise the file! any suggestion?

2015-02-02 16:50 GMT+01:00 Jennifer Hillman Jackson on Galaxy Biostar < notifications@biostars.org>:

ADD REPLY • link written 3.8 years ago by margherita.c86 • 0

Hello, 

Try opening IGV first (installed locally on your computer), then click on the IGV link. This usually resolves this issue when the link appears to be inactive.

Best, Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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