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HISAT2 output direct to bam sorted

Hi all, I am mapping my samples to a reference genome with HISAT2 and I was wondering if it is possible to get the outputs in bam format and also if it is possible to sort by coordinates directly?

Could you help me modify my command?

hisat2 --dta -x genome -1 ../fastq_zea_mays/SRR214880_1.fastq -2 ../fastq_zea_mays/SRR214880_2.fastq -S SRR214880.sam
sorted hisat2 bam to output direct
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updated by z • z • written by san96 • san96

1 answer 

hisat2 --dta -x genome -1 ../fastq_zea_mays/SRR214880_1.fastq -2 ../fastq_zea_mays/SRR214880_2.fastq \
| samtools sort -o sorted.bam
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written by ATpoint ATpoint

Thanks so much, what is the function of "\" ?

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written by san96 • san96

It's just a line break so I can write code into two lines for readability and structure. It's not necessary for function.

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written by ATpoint ATpoint

thanks very much

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written by z • z

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