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How i can get unalignment read in hisat2 ?

is there any option in hisat2 for viewing unalignment read? first: i make index for my refrence genome with this command:

 hisat2-build -p 3 Danio_rerio.GRCz11.cdna.all.fa /home/ngs/zebra_fish

second: i make alignment my fastq file with reference genome, using this command:

hisat2 -p 4 -x /home/ngs/zebra_fish/zebra_fish -U SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1.fastq -S SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1_chrl.sam

i get my output in .sam format, then i transfer it to bam file, using this command:

samtools view -bS SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1_chrl.sam > eg2.bam
after that i get my bam file

i read the manual of hisat2 and i cannot find any option to view the unalignment reads the question i how i can get my unalignment read and view it with readable way? Note: the data is RNA seq

hisat2
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updated by GenoMax GenoMax • written by Ahmed • Ahmed

I extract it from bam file but, how i can view it on terminal?

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written by Ahmed • Ahmed

To view the file contents, you can use any unix file command head/tail/cat/more etc if the file is uncompressed. Use zcat if the file is compressed.

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written by GenoMax GenoMax

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