Chris Allan

Hi Adam, Sorry for the delay. Hopefully your method worked. If you still want me to elaborate on what I did maybe send me an email at cjall6 (at) student.monash.edu and I will get back to you? Regards, Chris

Hi Robert and Adam, Yep, that's right there was 2 samples for my pileup file. I used samtools version 1.3.1 and STAR version 020201 for alignment; I will try another version of samtools to see if that was a problem. In the meantime I adapted a perl script, pileup2base.pl, to derive a sync file I can use with fst-sliding.pl. Regards, Chris

Hi, So I ran the perl version of mpileup2sync just to see what would happen. It got to a certain point then gave this error: Fucked entry dmel_mitochondrion_genome 19507 A 1 , < 0 at ../popoolation2_1201/Modules/Pileup.pm line 50, <$ifh> line 19507. Here is line 19506-8 of the pileup: dmel_mitochondrion_genome 19506 A 2 ,$, :E 2 ,$,$ B: dmel_mitochondrion_genome 19507 A 1 , < 0 dmel_mitochondrion_genome 19508 T 0 0 Does this mean something is wrong with my pileup? How could I fix it?

Hi Robert, So, I definitely set my fastq quality encoding to be sanger. Do you have any other suggestions as to why mpileup2sync is printing "null" at so many points of the sync file? I used star for my alignment of rna reads. Is popoolation2 compatible with bwa aligner only? Bwa isn't really splice-aware so that's why I used star. Any help would be really appreciated!

any other advice? :)

Hi Robert, Thanks for the advice, but I definitely did use sanger in the mpileup2sync.jar! java -jar /popoolation2_1201/mpileup2sync.jar --fastq-type sanger --min-qual 20 --threads 3 --output myfile.sync --input myfile.mpileup Cheers, Chris

If I run "zcat myfile.mpileup.gz | head -400 > mpileuphead.txt", I get the file attached. Does anything appear wrong with the mpileup file at the 171st base of the reference? Cheers, Chris

Hi Robert, I finally have some answers! So, the first lines of my sync file appear to be fine: dmel_mitochondrion_genome 1 A 5:0:0:0:0:0 2:0:0:0:0:0 dmel_mitochondrion_genome 2 A 6:0:0:0:0:0 4:0:0:0:0:0 dmel_mitochondrion_genome 3 T 0:7:0:0:0:0 0:6:0:0:0:0 dmel_mitochondrion_genome 4 G 0:0:0:20:0:0 0:0:0:30:0:0 dmel_mitochondrion_genome 5 A 20:0:0:0:0:0 33:0:0:0:0:0 But something goes wrong 170 bases into the reference genome, and the sync file is filled with null entries: dmel_mitochondrion_genome...