Galaxy problem
Dear all,
I' really new to the use of Galaxy, NGS analysis and SNP calling.
I have a problem.
Now I describe you my work step-by-step.
I have two fasta sequence one forward and one reverse.
I check with FastQC, result all ok.
I groomed them with FastQ grommer, all ok.
I map them whit BWA, all ok (bowtie gives me error).
After that I apply Filter SAM:
Input Parameter Value
Select dataset to filter -->10: Map with BWA for Illumina on data 8 and data 7: mapped reads
Type --> Read is paired; Set the states for this flag --> Yes
Type --> Read is mapped in a proper pair; Set the states for this flag --> Yes
Type --> The read is unmapped; Set the states for this flag --> No
All ok.
I convert SAM to BAM, no problem.
After that I generate pileup:
I leave all the setting as usual, I change only: Call consensus according to MAQ model? yes
Result: all ok.
Next: Filter pileup,
Input Parameter Value
Select dataset--> 13: Generate pileup on data 12: converted pileup
which contains--> ten
Do not consider read bases with quality lower than--> 20
Do not report positions with coverage lower than--> 3
Only report variants?--> Yes
Convert coordinates to intervals?--> Yes
Print total number of differences?--> No
Print quality and base string? --> No
Result: all ok.
The resulting data set contain about 2200 SNPs
At least I compare my result data set whit dbSNP132.txt and 1kg.lc.2010_7.CEU.liftedhg19.pgSnp.
The resulting data set contain 700 SNPs.
Now the question:
The problem is that I must have 200 SNPs and no 700....
I have check the resutls and I saw that some result are duplicated for all parameters but had a different rs ID.
how can I remove the wrong one???
please help me.
some one I heard about SOAPsnp but I don't know how to use. Could anyone please help me.
Thx Francesco
I' really new to the use of Galaxy, NGS analysis and SNP calling.
I have a problem.
Now I describe you my work step-by-step.
I have two fasta sequence one forward and one reverse.
I check with FastQC, result all ok.
I groomed them with FastQ grommer, all ok.
I map them whit BWA, all ok (bowtie gives me error).
After that I apply Filter SAM:
Input Parameter Value
Select dataset to filter -->10: Map with BWA for Illumina on data 8 and data 7: mapped reads
Type --> Read is paired; Set the states for this flag --> Yes
Type --> Read is mapped in a proper pair; Set the states for this flag --> Yes
Type --> The read is unmapped; Set the states for this flag --> No
All ok.
I convert SAM to BAM, no problem.
After that I generate pileup:
I leave all the setting as usual, I change only: Call consensus according to MAQ model? yes
Result: all ok.
Next: Filter pileup,
Input Parameter Value
Select dataset--> 13: Generate pileup on data 12: converted pileup
which contains--> ten
Do not consider read bases with quality lower than--> 20
Do not report positions with coverage lower than--> 3
Only report variants?--> Yes
Convert coordinates to intervals?--> Yes
Print total number of differences?--> No
Print quality and base string? --> No
Result: all ok.
The resulting data set contain about 2200 SNPs
At least I compare my result data set whit dbSNP132.txt and 1kg.lc.2010_7.CEU.liftedhg19.pgSnp.
The resulting data set contain 700 SNPs.
Now the question:
The problem is that I must have 200 SNPs and no 700....
I have check the resutls and I saw that some result are duplicated for all parameters but had a different rs ID.
how can I remove the wrong one???
please help me.
some one I heard about SOAPsnp but I don't know how to use. Could anyone please help me.
Thx Francesco