生成htseq-count的input文件

参考文章：RNA-seq(6): reads计数，合并矩阵并进行注释 - ；RNA-seq分析htseq-count的使用 - 望着小月亮 - 博客园

htseq-count -r name -f bam /mnt/f/rna_seq/aligned/SRR35899${i}_nsorted.bam /mnt/f/rna_seq/data/reference/annotation/mm10/gencode.vM10.chr_patch_hapl_scaff.annotation.gtf > /mnt/f/rna_seq/data/matrix/SRR35899${i}.count 2> /mnt/f/rna_seq/data/matrix/SRR35899${i}.log

for ((i=59;i<=62;i++));do htseq-count -r name -f bam /mnt/f/rna_seq/aligned/SRR35899${i}_nsorted.bam /mnt/f/rna_seq/data/reference/annotation/mm10/gencode.vM10.chr_patch_hapl_scaff.annotation.gtf > /mnt/f/rna_seq/data/matrix/SRR35899${i}.count;done

htseq-count -f bam -r name -s no -a 10 -t exon -i gene_id -m intersection-nonempty yourfile_name.bam ~/reference/hisat2_reference/Homo_sapiens.GRCh38.86.chr_patch_hapl_scaff.gtf > counts.txt

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samtools sort -o htseq-input-file/17F24T.sorted-by-n.bam -n -@12 aligned/17F24T/17F24T.sam

samtools sort -o htseq-input-file/105TRA.sorted-by-n.bam -n -@12 aligned/105TRA/105TRA.sam

samtools sort -o htseq-input-file/108TRA.sorted-by-n.bam -n -@12 aligned/108TRA/108TRA.sam

samtools sort -o htseq-input-file/109TRA.sorted-by-n.bam -n -@12 aligned/109TRA/109TRA.sam

samtools sort -o htseq-input-file/110A.sorted-by-n.bam -n -@12 aligned/110A/110A.sam

samtools sort -o htseq-input-file/112A.sorted-by-n.bam -n -@12 aligned/112A/112A.sam

samtools sort -o htseq-input-file/113A.sorted-by-n.bam -n -@12 aligned/113A/113A.sam

samtools sort -o htseq-input-file/114A.sorted-by-n.bam -n -@12 aligned/114A/114A.sam

samtools sort -o htseq-input-file/120A.sorted-by-n.bam -n -@12 aligned/120A/120A.sam

samtools sort -o htseq-input-file/121A.sorted-by-n.bam -n -@12 aligned/121A/121A.sam

samtools sort -o htseq-input-file/122A.sorted-by-n.bam -n -@12 aligned/122A/122A.sam

samtools sort -o htseq-input-file/124A.sorted-by-n.bam -n -@12 aligned/124A/124A.sam

samtools sort -o htseq-input-file/126A.sorted-by-n.bam -n -@12 aligned/126A/126A.sam

samtools sort -o htseq-input-file/127A.sorted-by-n.bam -n -@12 aligned/127A/127A.sam

samtools sort -o htseq-input-file/130A.sorted-by-n.bam -n -@12 aligned/130A/130A.sam

samtools sort -o htseq-input-file/136A.sorted-by-n.bam -n -@12 aligned/136A/136A.sam

samtools sort -o htseq-input-file/140A.sorted-by-n.bam -n -@12 aligned/140A/140A.sam

samtools sort -o htseq-input-file/143A.sorted-by-n.bam -n -@12 aligned/143A/143A.sam

samtools sort -o htseq-input-file/153A.sorted-by-n.bam -n -@12 aligned/153A/153A.sam

samtools sort -o htseq-input-file/154A.sorted-by-n.bam -n -@12 aligned/154A/154A.sam

---

htseq-count -f bam -r name htseq-input-file/17F24T.sorted-by-n.bam gencode.v31.annotation.gtf > 17F24T-counts.txt

---

htseq-count -f bam -r name htseq-input-file/17F24T.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/17F24T.count

htseq-count -f bam -r name htseq-input-file/105TRA.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/105TRA.count

htseq-count -f bam -r name htseq-input-file/108TRA.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/108TRA.count

htseq-count -f bam -r name htseq-input-file/109TRA.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/109TRA.count

htseq-count -f bam -r name htseq-input-file/110A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/110A.count

htseq-count -f bam -r name htseq-input-file/112A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/112A.count

htseq-count -f bam -r name htseq-input-file/113A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/113A.count

htseq-count -f bam -r name htseq-input-file/114A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/114A.count

htseq-count -f bam -r name htseq-input-file/120A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/120A.count

htseq-count -f bam -r name htseq-input-file/121A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/121A.count

htseq-count -f bam -r name htseq-input-file/122A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/122A.count

htseq-count -f bam -r name htseq-input-file/124A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/124A.count

htseq-count -f bam -r name htseq-input-file/126A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/126A.count

htseq-count -f bam -r name htseq-input-file/127A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/127A.count

htseq-count -f bam -r name htseq-input-file/130A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/130A.count

htseq-count -f bam -r name htseq-input-file/136A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/136A.count

htseq-count -f bam -r name htseq-input-file/140A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/140A.count

htseq-count -f bam -r name htseq-input-file/143A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/143A.count

htseq-count -f bam -r name htseq-input-file/153A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/153A.count

htseq-count -f bam -r name htseq-input-file/154A.sorted-by-n.bam gencode.v31.annotation.gtf > htseq-input-file/154A.count