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Question about Hisat-3N align #436

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bugandong opened this issue Jul 24, 2024 · 0 comments
Open

Question about Hisat-3N align #436

bugandong opened this issue Jul 24, 2024 · 0 comments

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@bugandong
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I used trimmed fastq file(the next generation sequencing) to align, why the reads length are still 150bp in the bam file? I choose a single example to show, the last two are the results of the align using Hisat-3n
trim_galore --trim-n --clip_R1 3 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3 -j 4 -q 20 --fastqc --paired --stringency 1 $pre_dir/00.rename/${i}_1.fq.gz $pre_dir/00.rename/${i}_2.fq.gz -o $pre_dir/01.filter >> $pre_dir/01.filter/trim.log 2>&1;
da079c9a160935ca8c62784c9f1c777

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