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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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read names changed? #85

Open patidarr opened 7 years ago

patidarr commented 7 years ago

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

divy-kangeyan commented 7 years ago

My guess would be that you need to use the same random seed using -s handle.