From 2946c626b7b47ab8edfcaec41ed48658e80da001 Mon Sep 17 00:00:00 2001 From: Alan Hoyle Date: Tue, 9 Aug 2022 16:58:36 -0400 Subject: [PATCH] fixed README.md formatting --- README.md | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index acd2379..9608410 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ BCR heavy (IgH) and light (Igk/IgL) chains. V'DJer accepts a sorted and indexed BAM file mapped to hg38 as input. We currently use STAR for alignment. At the end of a run assembled contigs will appear in -```vdj_contigs.fa``` and reads aligned to those contigs are written to ```stdout``` +`vdj_contigs.fa` and reads aligned to those contigs are written to `stdout` The V'DJer output is suitable for use by downstream quantification tools such as [RSEM](http://deweylab.github.io/RSEM/). @@ -16,8 +16,8 @@ The V'DJer output is suitable for use by downstream quantification tools such as Use a recent release: https://github.com/mozack/vdjer/releases -To compile, just cd into the vdjer directory and type ```make```. An executable named -```vdjer``` will be created. +To compile, just cd into the vdjer directory and type `make`. An executable named +`vdjer` will be created. To date, V'DJer has been tested only on linux systems. @@ -33,14 +33,16 @@ V'DJer operates on paired end reads. Single end reads are not currently support When mapping with STAR, unmapped reads must be included in the BAM file (this is not STAR's default behavior). Include the unmapped reads using the following param: -```--outSAMunmapped Within``` +`--outSAMunmapped Within` Be sure to sort and index the BAM file. The following runs vdjer on the input star.sort.bam file with vdj_contigs.fa generated in the current working directory and read alignments written to vdjer.sam: -```vdjer --in star.sort.bam --t 8 --ins 175 --chain IGH --ref-dir vdjer_human_references/igh > vdjer.sam 2> vdjer.log``` +``` +vdjer --in star.sort.bam --t 8 --ins 175 --chain IGH --ref-dir vdjer_human_references/igh > vdjer.sam 2> vdjer.log +``` The above runs on the IgH chain with read length of 50, 8 threads and median insert length of 175. @@ -59,8 +61,10 @@ In cases where a sample has low BCR expression levels, one may opt to run V'DJer Running sensitive mode on samples with abundant BCR expression levels may result in extremely high computational costs. Example command: -```vdjer --in star.sort.bam --t 8 --ins 175 --chain IGH --ref-dir vdjer_human_references/igh --k 25 ---mq 60 --mf 2 --rs 25 --ms 2 --mcs -5.5 > vdjer.sam 2> vdjer.log ``` +``` +vdjer --in star.sort.bam --t 8 --ins 175 --chain IGH --ref-dir vdjer_human_references/igh --k 25 +--mq 60 --mf 2 --rs 25 --ms 2 --mcs -5.5 > vdjer.sam 2> vdjer.log +``` Decreasing mq and mf from the defaults results in less aggressive graph pruning. Reducing rs and ms results in less aggressive coverage based filtering