直接下载的是clean_data所以跳过质控直接做map,修改了代码如下
for i in SRR9113321 SRR9113322 SRR9113323 SRR9113324 SRR9113325 SRR9113326 SRR9113327 SRR9113328 SRR9113329 SRR9113330 SRR9113331 SRR9113332 SRR9113333; do
echo "RUN CMD: hisat2 -p 1 --rg-id=${i} --rg SM:${i} --rg LB:${i} --rg PL:ILLUMINA \
-x $REF_INDEX --dta --rna-strandness RF \
-1 $workdir/data/${i}_1.fastq.gz \
-2 $workdir/data/${i}_2.fastq.gz \
-S ${i}.sam 2>${i}.summary"
hisat2 -p 1 --rg-id=${i} --rg SM:${i} --rg LB:${i} --rg PL:ILLUMINA \
-x $REF_INDEX --dta --rna-strandness RF \
-1 $workdir/data/${i}_1.fastq.gz \
-2 $workdir/data/${i}_2.fastq.gz \
-S ${i}.sam 2>${i}.summary
done
最后出现结果文档报错
(ERR): "--dta" does not exist
Exiting now ...
请问怎么解决
