SOLiD PE 50/25 50/35 mapping using BFAST

[Patidar]

Hi,
I am running BFAST on SOLiD PE data, the workflow is:
Indexing of hg19 using 10 masks in BFAST pdf 7.1.2

Solid2fastq (bfast version)
Give the following output:

Outputting, currently on:
105443471
Found
number_of_ends number_of_reads
1 0
2 105443471

Then I do mapping using default parameters but the Number of reads mapped with 2 ends mapped (postprocess STDOUT)is strange:
Found 1330976 reads with 2 ends mapped.
Found 1352354 reads with 2 ends mapped.
Found 739903 reads with 2 ends mapped.
Found 2092482 reads with 2 ends mapped.
Found 1834718 reads with 2 ends mapped.
Found 1835699 reads with 2 ends mapped.
Found 2068385 reads with 2 ends mapped.
Found 1070307 reads with 2 ends mapped.
Found 2232393 reads with 2 ends mapped.
Found 2293698 reads with 2 ends mapped.
Found 1747380 reads with 2 ends mapped.

This is like ~18 reads are PE but the solid2fastq says all the reads are PE.

Any Help is highly appreciated!!

[nilshomer]

What was your postprocess command line? Did you set the paired end options?

[Patidar]

Hi Nils,

I am running in PE mode i.e. Y=0 and the I am setting PE to 170 and PI SD to 50.

Thanks,

[nilshomer]

When you look at a few mappings, are they correctly orientated? Perhaps the input was reverse complimented or the order was switched?

[Patidar]

I mapped the same sample using bioscope and the PE % was much higher. and the stats from bioscope says that the PI is from 150-250. So I guess the % should drop but not that much.

Also I ran the same sample with PI 180 and PI SD 20 and the Stats after postprocessing are exactly the same. not even a single decrease or increase in number.

If the order is switched, solid2fastq will complain or not ?
I have not looked into the bam. Silly Question How to know if the reads are RC from Bam ?


Thanks.

[nilshomer]

Look at the SAM file produced by BFAST. See if pairs are on the correct strand and within the insert size range.