Hello all,
I am attempting to process a published Solexa RNAseq dataset, but I am running into some issues due to the base quality encoding.
***This is the code I am using to attempt to trim adapter sequences:
$HOME/adapterremoval/bin/AdapterRemoval --qualitybase solexa --file1 $raw_files_path/$input_filename_1 \
--file2 raw_files_path/$input_filename_2 --basename $input_filename --trimns --trimqualities --gzip \
--adapter-list $HOME/RNAseq/adapters_set1.txt
***and this is the error I keep getting.
Read 2 adapters / adapter pairs from '/mnt/home/username/RNAseq/adapters-set1.txt'...
Trimming paired end reads ...
Error reading FASTQ record at line 1; aborting:
Phred+64 encoded quality score is less than 0 (ASCII < '@');
Are these FASTQ reads actually in Phred+33 format? If so,
use the command-line option "--qualitybase 33"
See README for more information.
I am not sure what to do, as the software is detecting quality scores that are less than zero (indicating Solexa encoding), but refusing to process the data even though I have specified "--qualitybase solexa" (as recommended in the user manual).
Normally I use Trimmomatic for adapter trimming, but I have successfully used AdapterRemoval (https://github.com/MikkelSchubert/ad...terRemoval.pod) in the past on Illumina Hiseq data.
Please help!!!
Thank You!!!
I am attempting to process a published Solexa RNAseq dataset, but I am running into some issues due to the base quality encoding.
***This is the code I am using to attempt to trim adapter sequences:
$HOME/adapterremoval/bin/AdapterRemoval --qualitybase solexa --file1 $raw_files_path/$input_filename_1 \
--file2 raw_files_path/$input_filename_2 --basename $input_filename --trimns --trimqualities --gzip \
--adapter-list $HOME/RNAseq/adapters_set1.txt
***and this is the error I keep getting.
Read 2 adapters / adapter pairs from '/mnt/home/username/RNAseq/adapters-set1.txt'...
Trimming paired end reads ...
Error reading FASTQ record at line 1; aborting:
Phred+64 encoded quality score is less than 0 (ASCII < '@');
Are these FASTQ reads actually in Phred+33 format? If so,
use the command-line option "--qualitybase 33"
See README for more information.
I am not sure what to do, as the software is detecting quality scores that are less than zero (indicating Solexa encoding), but refusing to process the data even though I have specified "--qualitybase solexa" (as recommended in the user manual).
Normally I use Trimmomatic for adapter trimming, but I have successfully used AdapterRemoval (https://github.com/MikkelSchubert/ad...terRemoval.pod) in the past on Illumina Hiseq data.
Please help!!!
Thank You!!!
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