I am looking for advice on the output of
SolexaQA++ lengthsort - c when preprocessing my RNA-Seq data.
Having already used
SolexaQA++ dynamictrim to trim by read quality I then sought to remove any short reads which resulted using
SolexaQA++ lengthsort and as the data is paired end I used the
Here are the relevant lines from my bash script:
path1="/PATH/TO/trim/Sample1_R1" path2="/PATH/TO/trim/Sample1_R2" SolexaQA++ lengthsort -c -l 36 -d "/PATH/TO/sort" $path1$".fastq.trimmed.gz", $path2$".fastq.trimmed.gz"
I expected there to be six resulting files; paired-end, singleton and discard for each input file (R1 and R2). However what was produced was just two
Sample1_R2.trimmed.gz.paired. What happened to R1?
Has something gone wrong? if so how? and if not what do these files contain?
If it helps the input files are trimmed FASTQ files. Here is the top 8 lines of
Sample1_R1.fastq.trimmed when unzipped.
@HWI-7001326F:29:C732HANXX:8:1101:1258:1926 1:N:0:ATCACGAT TCATGAGAAAAGGAACTCCGTCTCATCTGGCATTGCCAATAAAC + FFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @HWI-7001326F:29:C732HANXX:8:1101:1457:1985 1:N:0:ATCACGAT CAACAACTTTGAAGGGTCTTGAAAGGGCAGGTAGTCCTCTAACTGAAGATTTCTCAACTCTAAAAGGAGTTGGTTTCAAACTCACAGAAGCCATAACTGAAGAGATCGGAAGAGCACACG + BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB
The output files both appear to be empty.
This was the end of the terminal output:
... Cleaned from read 2: @HWI-7001326F:29:C732HANXX:8:2316:20703:101335 Cleaned from read 2: @HWI-7001326F:29:C732HANXX:8:2316:20624:101360 Cleaned from read 2: @HWI-7001326F:29:C732HANXX:8:2316:20904:101266 Cleaned from read 2: @HWI-7001326F:29:C732HANXX:8:2316:20879:101307 Cleaned from read 2: @HWI-7001326F:29:C732HANXX:8:2316:20776:101348 Cleaned from read 2: @HWI-7001326F:29:C732HANXX:8:2316:20940:101369 Paired reads were written to: /PATH/TO/sort/.clean /PATH/TO/sort/C732HANXX-1721-01-01-01_L008_R2.fastq.trimmed.gz.clean 100% [==================================================] Writing files...
Why has this happened?