Edited reads can be extracted from "tmp/all_combined.zz".
Finally, users can apply SPRINT to the unaligned reads (FASTQ format) to obtain hyper RESs and hyper-edited reads. However, in order to detect hyper RESs from BAM format, users can use SAMTOOLS to extract unaligned reads (BAM format) with command options of “samtools view -f4 -b”, and then convert it into FASTQ format with command options of “samtools bam2fq”. In exchange, “sprint_from_bam” doesn’t include the function of detecting hyper RESs, because detecting hyper RESs needs to use aligner. “sprint_from_bam” was designed for aligned reads without using any aligner. The reference_genome used by sprint_from_bam should be the same with that used by alignerĭ. Please remember that sprint_from_bam only uses reads with proper MAPQ (from 20 to 200) to detect RESs.Ĭ. You can use changeSAMmapQ.py ( ) to change the MAPQ of your SAM files generated by other aligner (except BWA). Before using "sprint_from_bam", BAM file should be sorted by using samtools ("samtools sort").ī. Generated by using rp2bed.py (see Tips below, script is in ) Attention:Ī. Sprint_from_bam | | aligned_reads(.bam) | reference_genome(.fa) | output_path | samtools_pathĭetails about "options" are in SPRINT_manual.pdf ( ) Sprint main | | reference_genome(.fa) | output_path | bwa_path | samtools_path Sprint prepare | | reference_genome(.fa) | bwa_path 2018, 0.1.7 - first version on github Citation:įeng Zhang, Yulan Lu, Sijia Yan, Qinghe Xing, Weidong Tian SPRINT: an SNP-free toolkit for identifying RNA editing sites, Bioinformatics, Volume 33, Issue 22, 15 November 2017, Pages 3538–3548, Requirement: SAMTOOLS = 1.2 & BWA = 0.7.12 Unix & Python2.7 Do not use. 2019, new feature (>=0.1.8) is only on Github, please do not use "pip install sprint" to install the latest SPRINT.įeb. SPRINT is designed for detecting RNA editing sites from RNA-seq data RES (dbRES) & Repeat Region (dbREP) The active grid-capture lets you place your elements exactly.SNP-free RNA editing Identification Toolkit (SPRINT) are always visible at a glance, and can be edited every time. All parameter like track-width, pad-size, etc. Just select the corresponding mode and place your elements. Sprint-Layout is equipped with tools to draw pads, tracks, copper areas, labels and so on. Sprint-Layout is also able to create HPGL files for isolation-milling. If required, you can export your layout to the GERBER and EXCELLON format. If you want to produce professional boards, there are many PCB-manufacturers, which accept Sprint-Layout files. For manufacturing your PCB's by hand, there is an excellent printout-procedure with many options available. Sprint-Layout offers all needed functions to design your own layouts.
You can concentrate to the essential thing Designing and optimizing your PCB-layouts. There is no unnecessary "ballast" which makes it difficult to keep the overview or which makes the usage almost impossible.
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