Closed hemingwang closed 5 years ago
Hi, Couly you upload your commond and head of your fq file? THX
Hi Junchao, my code is: sports.pl -i ~/smallrna/S1_trimmed.fastq -p 12 -a -x GTTCAGAGTTCTACAGTCCGACGATC -y AGATCGGAAGAGCACACGTCT -g ~/smallrna/qi/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/genome -m ~/smallrna/qi/Homo_sapiens/miRBase_21/miRBase_21-hsa -r ~/smallrna/qi/Homo_sapiens/rRNAdb/human_rRNA -t ~/smallrna/qi/Homo_sapiens/GtRNAdb/hg19-tRNAs -w ~/smallrna/qi/Homo_sapiens/piRBase/piR_human -e ~/smallrna/qi/Homo_sapiens/Ensembl/Homo_sapiens.GRCh38.ncrna -f ~/smallrna/qi/Homo_sapiens/Rfam_12.3/Rfam-12.3-human -o ~/smallrna/qi/out -k
head of the fq: @E00515:299:HJY52CCXY:4:1101:2209:1801 1:N:0:ATCACGAT CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACGCAAGGGTTTGTA + <AAFA<AFJ--AAJF<JJFJFJJAF7FFJJAFA-FAF-FFFF7F-7 @E00515:299:HJY52CCXY:4:1101:3488:1801 1:N:0:ATCACGAT AGACTGTGTTTT + <AAFFJJJJJFJ @E00515:299:HJY52CCXY:4:1101:4584:1801 1:N:0:ATCACGAT CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGT
Best wishes! heming wang
It looks like your fastq file is already trimmed so that -a -x -y is not necessary. Could you run it again and theck the processing report to see what exact happens?
Thanks for your patience helping me! I run it again.
Hi Junchao, I am ran the sports.pl and produce the results. But when I run the annotation.pl, I meet the wrong:
Can't open '/smallrna/qi/out.fa': No such file or directory at annotation.pl line 33.
my sports.pl file is in the "/smallrna/qi/",named "out". The "out" file contain "1_S1_trimmed","processing_report","sh_file" and "run_this.sh"
I am looking forward to your reply!
Best wishes! heming wang