From 7318deb1ad65796fb72b15392e782e093a64e5e2 Mon Sep 17 00:00:00 2001 From: Hasindu Gamaarachchi Date: Fri, 12 Apr 2024 21:36:54 +1000 Subject: [PATCH] set the parameters in the rna004-min profile --- docs/profile.md | 16 ++++++++-------- src/sim.c | 13 ++++++------- 2 files changed, 14 insertions(+), 15 deletions(-) diff --git a/docs/profile.md b/docs/profile.md index fa5cce2..eb1876c 100755 --- a/docs/profile.md +++ b/docs/profile.md @@ -43,16 +43,16 @@ These profile sets the following advanced parameters in squigulator. | Parameter | dna-r10-min | dna-r10-prom | rna004-min | rna004-prom | |---------------------|---------------|-----------------|--------------|---------------| -| digitisation | 8192 | 2048 | 2048 | 2048 | +| digitisation | 8192 | 2048 | 8192 | 2048 | | sample-rate | 4000 | 4000 | 4000 | 4000 | | bps | 400 | 400 | 130 | 130 | -| range | 1536.598389 | 281.345551 | TBD | 299.432068 | -| offset-mean | 13.380569389 | -127.5655735 | TBD5 | -259.421128 | -| offset-std | 16.311471649 | 19.377283387665 | TBD | 16.010841823643 | -| median-before-mean | 202.154074388 | 189.87607393756 | TBD | 189.87607393756 | -| median-before-std | 13.406139242 | 15.788097978713 | TBD | 15.788097978713 | -| dwell-mean | 10.0 | 10.0 | TBD | 31.0 | -| dwell-std | 4.0 | 4.0 | TBD | 4.0 | +| range | 1536.598389 | 281.345551 | 1437.976685 | 299.432068 | +| offset-mean | 13.380569389 | -127.5655735 | 12.47686423863 | -259.421128 | +| offset-std | 16.311471649 | 19.377283387665 | 10.442126577137 | 16.010841823643 | +| median-before-mean | 202.154074388 | 189.87607393756 | 205.08496731088 | 189.87607393756 | +| median-before-std | 13.406139242 | 15.788097978713 | 8.6671292866233 | 15.788097978713 | +| dwell-mean | 10.0 | 10.0 | 31.0 | 31.0 | +| dwell-std | 4.0 | 4.0 | 0.0 | 0.0 | ## Determining parameters for a profile diff --git a/src/sim.c b/src/sim.c index ac8ee72..9eeb96a 100644 --- a/src/sim.c +++ b/src/sim.c @@ -140,11 +140,11 @@ profile_t minion_rna004_rna_prof = { .digitisation = 8192, .sample_rate = 4000, .bps = 130, - .range = 1536.598389, - .offset_mean=13.380569389019, - .offset_std=16.311471649012, - .median_before_mean=202.15407438804, - .median_before_std=13.406139241768, + .range = 1437.976685, + .offset_mean=12.47686423863, + .offset_std=10.442126577137, + .median_before_mean=205.08496731088, + .median_before_std=8.6671292866233, .dwell_mean=31.0, //this must be sample_rate/bps for now .dwell_std=0.0 }; @@ -172,8 +172,7 @@ static inline profile_t set_profile(char *prof_name, opt_t *opt){ opt->flag |= SQ_R10; return minion_r10_dna_prof; }else if(strcmp(prof_name, "rna004-min") == 0){ - ERROR("%s","Parameters not determined for rna004 MinION. Please share some data!"); - exit(EXIT_FAILURE); + WARNING("%s","Parameters and models for rna004-min are still crude. If you have good IVT data, please share!"); opt->flag |= SQ_R10; opt->flag |= SQ_RNA; return minion_rna004_rna_prof;