From 39e2141e6685808240b31a6ec35132917c30d21c Mon Sep 17 00:00:00 2001 From: mstubb Date: Fri, 27 Nov 2015 11:39:25 +0000 Subject: [PATCH] README improvement --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 107b85a..a40c0f3 100644 --- a/README.md +++ b/README.md @@ -129,7 +129,7 @@ Tracer has two modes *assemble* and *summarise*. `-c/--config_file ` : config file to use. Default = `tracer.conf` `-s/--species` : Species from which the T cells were derived. Options are `Mmus` or `Hsap` for mouse or human data. This is only important for determination of iNKT cells in the `summarise` step because it defines the V segments that are indicative of iNKT cells. Default = `Mmus`. `-r/--resume_with_existing_files` : if this is set, TraCeR will look for existing output files and not re-run steps that already appear to have been completed. This saves time if TraCeR died partway through a step and you want to resume where it left off. -`-m/--seq_method` : method by which to generate sequences for assessment of recombinant productivity. By default (`-m imgt`), TraCeR replaces all but the junctional sequence of each detected recombinant with the reference sequence from IMGT prior to assessing productivity of the sequence. This makes the assumption that sequence changes outside the junctional region are due to PCR/sequencing errors rather than being genuine polymorphisms. This is likely to be true for well-characterised mouse sequences but may be less so for human and other outbred populations. To determine productivity from only the assembled contig sequence for each recombinant use `-m assembly`. +`-m/--seq_method` : method by which to generate sequences for assessment of recombinant productivity. By default (`-m imgt`), TraCeR replaces all but the junctional sequence of each detected recombinant with the reference sequence from IMGT prior to assessing productivity of the sequence. This makes the assumption that sequence changes outside the junctional region are due to PCR/sequencing errors rather than being genuine polymorphisms. This is likely to be true for well-characterised mouse sequences but may be less so for human and other outbred populations. To determine productivity from only the assembled contig sequence for each recombinant use `-m assembly`. `--single_end` : use this option if your data are single-end reads. If this option is set you must specify fragment length and fragment sd as below. `--fragment_length` : Estimated average fragment length in the sequencing library. Used for Kallisto quantification. Required for single-end data. Can also be set for paired-end data if you don't want Kallisto to estimate it directly. `--fragment_sd` : Estimated standard deviation of average fragment length in the sequencing library. Used for Kallisto quantification. Required for single-end data. Can also be set for paired-end data if you don't want Kallisto to estimate it directly.