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!!
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!!
Comment