Hisat2 error

Question

[sherafzalk769]

Hi all

I am using this command.

hisat2 -p 8 -q -X ${READDIR}/hisat2_index_Cm_genome  -1 ${READDIR}/tr.p.UE-2955-CMLib1_S88_L004_R1_001.fastq.gz -2 ${READDIR}/tr.p.UE-2955-CMLib1_S88_L004_R2_001.fastq.gz -S ${Output}/UE-2955-CMLib1.sam

Error: Encountered internal HISAT2 exception (#1)

Need a help to fix this problem.

thanks

[sherafzalk769]

I used the hisat2 to get the sam file but now I am using the samtools view to convert it to bam. I am getting this following error..

[main_samview] fail to read the header from "-"

Need suggestion

thanks

[ATpoint]

Which command line did you use? Please get used to always provide it when posting questions.

Answer 1

[ATpoint]

It is a lowercase x, so -x for the index.

[sherafzalk769]

thanks. it works now

[sherafzalk769]

thanks, it works

[Ram]

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