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ZhangLabSZ / RES-Scanner2

RES-Scanner 2 is a software package for genome-wide identification and annotation of RNA-editing sites for any species with matched RNA-Seq and DNA-Seq data.
MIT License
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RES-Scanner uses bam file to directly identify RNA editing sites, and reports an error. #2

Open 565755044 opened 1 year ago

565755044 commented 1 year ago

Hello, Teacher Guo, I didn't find the section for submitting questions in your github, so I posted it here (https://github.com/ZhangLabSZ/RES-Scanner2/issues/). I didn't choose the original transcriptome sequencing data as the input, but directly used the bam file (processed by samtools) compared with bowtie2 software as the input of the identification site. However, when using bestUniqForSam.pl to generate sort.rmdup.best.bam, there will be a problem of "'is recognized as' *'. [main samview] truncated file." I use version 2.10 of hisat2, version 0.1.18 of samtools and version 2.5 of bowtie2. The parameter of hisat2 is "Hisat2-x.dna.toplevel-1clean 1.fq.gz-2clean _ 2.fq.gz-no-mixed-no-discordant-p 8-s.sam" and the parameter of Bowtie2 is "Bowtie2-align". asic-0 -D 20 -R 22 --local -N 0.08 -L 32 -k 3 -p 8 -t -x GRCg7b -S b2XWRNA111 -U clean_1.fq.gz,clean_2.fq.gz”。 Both of these softwares are mentioned in the manual of RES-Scanner. Have you encountered similar problems? What are the requirements for custom comparison input? Looking forward to your reply.

Good wishes! Lv Jiayu Eighteen billion ninety-one million nine hundred and ninety thousand seven hundred and twenty-four

tomatoes111 commented 3 months ago

I also encountered this problem, how did you solve it afterwards？

565755044 commented 3 months ago

我也遇到过这个问题，后来你是怎么解决的？

Hi, you can probably try to fix the problem by changing the ‘--uniqTag 1’ parameter.

tomatoes111 commented 3 months ago

Hello friend, thank you very much, I'll give it a try right away,

tomatoes111 commented 3 months ago

Hello, I submitted the task and ran for a while, is it normal to have such a warning, "[bam_rmdup_core] inconsistent BAM file for pair 'E150012939L1C026R0361640741'. Continue anyway.", there are no errors yet, and I'll have to wait for it to run again to see if this will work