Hi,
The aim of my work now is to find SNPs in my dataset from Illumina GAII ( paired end) but when tried to filter pileup got this:
16: Filter pileup on data 14
An error occurred running this job: Use of uninitialized value in subroutine entry at /galaxy/home/g2main/galaxy_main/tools/samtools/pileup_parser.pl line 40, <IN> line 1.
Use of uninitialized value in numeric lt (<) at /galaxy/home/g2main/galaxy_main/tools/samtools/pileup_parser.pl line 41
I'm new Galaxy user, working with this kind of data for the first time...
I just had a first go and got an error... Could you please direct me on a right way of doing it as I must did something totally wrong
What I was doing:
-uploaded data in fastq format
-FASTQ groomer (Illumina 1.3+)
-FASTQ summary statistics
-FASTQ splitter
-Map with Bowtie for Illumina (paired end, typed my insert size)
-Filter SAM (flag1-read is paired YES; flag2-read is mapped in a proper pair-YES; flag3-read is umpapped-NO)
-SAM to BAM
-Generate pileup from BAM dataset
-Filter pileup
(not sure if I should have trimmed the reads first...)
I probably have been doing this all wrong from the beginning, so if anyone could tell me, what should I do to get the right thing would be great
The aim of my work now is to find SNPs in my dataset from Illumina GAII ( paired end) but when tried to filter pileup got this:
16: Filter pileup on data 14
An error occurred running this job: Use of uninitialized value in subroutine entry at /galaxy/home/g2main/galaxy_main/tools/samtools/pileup_parser.pl line 40, <IN> line 1.
Use of uninitialized value in numeric lt (<) at /galaxy/home/g2main/galaxy_main/tools/samtools/pileup_parser.pl line 41
I'm new Galaxy user, working with this kind of data for the first time...
I just had a first go and got an error... Could you please direct me on a right way of doing it as I must did something totally wrong
What I was doing:
-uploaded data in fastq format
-FASTQ groomer (Illumina 1.3+)
-FASTQ summary statistics
-FASTQ splitter
-Map with Bowtie for Illumina (paired end, typed my insert size)
-Filter SAM (flag1-read is paired YES; flag2-read is mapped in a proper pair-YES; flag3-read is umpapped-NO)
-SAM to BAM
-Generate pileup from BAM dataset
-Filter pileup
(not sure if I should have trimmed the reads first...)
I probably have been doing this all wrong from the beginning, so if anyone could tell me, what should I do to get the right thing would be great
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