I ran seqtk to convert the encoding on some fastq files I am having issues while running GATK using the command.
gunzip -c R1.fastq.gz >R1.fastq &
gunzip -c R2.fastq.gz >R2.fastq &
wait
module load seqtk
seqtk seq -Q64 -V R1.fastq >R1.fixed.fastq &
seqtk seq -Q64 -V R2.fastq >R2.fixed.fastq &
wait
Then I am trying to run STAR following way:
STAR --outTmpDir STEP1 --genomeDir STAR_hg19_index --readFilesIn R1.fixed.fastq R2.fixed.fastq --outFileNamePrefix D1D34ACXX --runThreadN ${THREADS} --outFilterMismatchNmax 2
but getting Error message:
ERROR_00201: EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >
Could you please let me know if I am running seqtk the correct way or not?
Hi,
I ran seqtk to convert the encoding on some fastq files I am having issues while running GATK using the command. gunzip -c R1.fastq.gz >R1.fastq & gunzip -c R2.fastq.gz >R2.fastq & wait module load seqtk seqtk seq -Q64 -V R1.fastq >R1.fixed.fastq & seqtk seq -Q64 -V R2.fastq >R2.fixed.fastq & wait
Then I am trying to run STAR following way: STAR --outTmpDir STEP1 --genomeDir STAR_hg19_index --readFilesIn R1.fixed.fastq R2.fixed.fastq --outFileNamePrefix D1D34ACXX --runThreadN ${THREADS} --outFilterMismatchNmax 2
but getting Error message: ERROR_00201: EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >
Could you please let me know if I am running seqtk the correct way or not?
Thansk, Rajesh