Hi
I'm trying to use SOAPdenovo with 14 paired end 500bp Illumina FQ files (7 files of each end). I tried to follow the example.config file on the SOAPdenovo website here
In my config file, I am specifying all my PE files as a single library since all have the same insert size. In that one library though, how do I specify my different PE files? I had specified them as (q1, q2) (q3, q4 ) and so on, but SOAPdenovo only looks at q1 and q2 files.
In the output, SOAPdenovo is looking only at q1 and q2. Is my config file correct?
My questions are:
1) Should I specify each PE set as q1,q2 in the same library? OR
2) Does each PE set need to be specified as a different library, each with its own q1, q2?
3) Any other solution??
I'd appreciate your help!
Thanks
Flobpf
I'm trying to use SOAPdenovo with 14 paired end 500bp Illumina FQ files (7 files of each end). I tried to follow the example.config file on the SOAPdenovo website here
In my config file, I am specifying all my PE files as a single library since all have the same insert size. In that one library though, how do I specify my different PE files? I had specified them as (q1, q2) (q3, q4 ) and so on, but SOAPdenovo only looks at q1 and q2 files.
Code:
#maximal read length max_rd_len=70 [LIB] #average insert size avg_ins=516 #if sequence needs to be reversed reverse_seq=0 #in which part(s) the reads are used asm_flags=3 #in which order the reads are used while scaffolding rank=1 #fastq file for read 1 q1=s_1_1_sequence.txt.trim70.gz #fastq file for read 2 always follows fastq file for read 1 q2=s_1_2_sequence.txt.trim70.gz #### #fastq file for read 1 q3=s_2_1_sequence.txt.trim70.gz #fastq file for read 2 always follows fastq file for read 1 q4=s_2_2_sequence.txt.trim70.gz #### #fastq file for read 1 q5=s_3_1_sequence.txt.trim70.gz #fastq file for read 2 always follows fastq file for read 1 q6=s_3_2_sequence.txt.trim70.gz
My questions are:
1) Should I specify each PE set as q1,q2 in the same library? OR
2) Does each PE set need to be specified as a different library, each with its own q1, q2?
3) Any other solution??
I'd appreciate your help!
Thanks
Flobpf
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