HTS (NGS) 関連のインフォマティクス情報についてまとめています。

一塩基変異や逆転写酵素によるアレストイベントを検出する JACUSA2







v2.0.2 static binaryをリリースからダウンロードしてテストした(openjdk 11.0.1環境)。


  • tested JACUSA2 with Java v1.8


> java -jar JACUSA_v2.0.2-RC.jar 



  call-1    Call variants - 1 condition

  call-2    Call variants - 2 conditions

  pileup    SAMtools like mpileup - 2 conditions

  rt-arrest    Reverse Transcription Arrest - 2 conditions

  lrt-arrest    Linkage arrest to base substitution - 2 conditions

Version:    2.0.2-RC

Libraries:     htsjdk 2.12.0, Apache commons-cli 1.4, Apache commpon-math3 3.6.1

java -jar JACUSA_v2.0.2-RC.jar call-1

usage: JACUSA call-1 [OPTIONS] BAM1_1[,BAM1_2,...]

 -A                    Show all sites - including sites without variants

 -a <FEATURE-FILTER>   [...] Use -h to see extended help

 -B <READ-TAG>         Tag reads by base substitution.

                       Count non-reference base substitution per read and stratify.

                       Requires stranded library type.

                       (Format for T to C mismatch: T2C; use ',' to separate substitutions)

                       Default: none

 -b <BED>              BED file to scan for variants

 -c <MIN-COVERAGE>     filter positions with coverage < MIN-COVERAGE

                       default: 5

 -D                    Show deletion score

 -d <MAX-DEPTH>        max read depth

                       default: -1

 -f <OUTPUT-FORMAT>    Choose output format:

                       <*> B: BED6-extended result format

                       < > V: VCF Output format. Option -P will be ignored (VCF is unstranded)

 -F <FLAG>             filter reads with flags FLAG

                       default: 0

 -filterNH <NH>        Max NH-VALUE for SAM tag NH for all conditions

 -filterNM <NM>        Max NM-VALUE for SAM tag NM for all conditions

 -h                    Print extended usage information

 -I                    Show insertion score

 -m <MIN-MAPQ>         filter positions with MAPQ < MIN-MAPQ

                       default: -1

 -p <THREADS>          use # THREADS

                       default: 1

 -P <LIB-TYPE>         Choose the library type for all conditions:

                       RF-FIRSTSTRAND    STRANDED library - first strand sequenced

                       FR-SECONDSTRAND    STRANDED library - second strand sequenced

                       UNSTRANDED        UNSTRANDED library

                       default: UNSTRANDED

 -q <MIN-BASQ>         filter positions with base quality < MIN-BASQ

                       default: 20

 -R <REF-FASTA>        use reference FASTA file (must be indexed)

 -r <RESULT-FILE>      results are written to RESULT-FILE

 -s                    Store feature-filtered results in another file (= RESULT-FILE.filtered if no argument) or (= FILTERED-FILE)

 -T <THRESHOLD>        Filter positions based on test-statistic THRESHOLD

                       default: DO NOT FILTER

 -u <MODE>             [...] Use -h to see extended help

 -w <WINDOW>           size of the window used for caching. Make sure this is greater than the read size

                       default: 10000

 -W <THREAD-WINDOW>    size of the window used per thread

                       default: 100000






java -jar jacusa2.jar call-1 -r results_call1.out -p 12 alignments.bam
  • -p      use # THREADS
  •  -r     results are written to RESULT-FILE



java -jar jacusa2.jar call-2 results_call2.out condition1.bam condition2.bam


  • JACUSA2helper   JACUSA2出力のダウンストリーム解析をサポートするRのヘルパーの新しいバージョン。アーテファクトのフィルタリングなどを行う。



RNA modification mapping with JACUSA2
Michael Piechotta, Isabel S. Naarmann-de Vries, Qi Wang, Janine Altmüller & Christoph Dieterich 
Genome Biology volume 23, Article number: 115 (2022)