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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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question about annotation.pl #2

Closed hemingwang closed 5 years ago

hemingwang commented 5 years ago

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

junchaoshi commented 5 years ago

Hi, Couly you upload your commond and head of your fq file? THX

hemingwang commented 5 years ago

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

junchaoshi commented 5 years ago

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?

hemingwang commented 5 years ago

Thanks for your patience helping me! I run it again.