From 4d72de3fb0e9d4848d54ed574d9280f64af84ce2 Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 7 Dec 2015 15:59:27 +0000 Subject: [PATCH 1/2] fixing the category for a track (mistake put it in "General" and gave it a extra bogus subtrack) --- snyder_conf/snyder_gfp_tf.conf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snyder_conf/snyder_gfp_tf.conf b/snyder_conf/snyder_gfp_tf.conf index 5db5eda..1e217f7 100644 --- a/snyder_conf/snyder_gfp_tf.conf +++ b/snyder_conf/snyder_gfp_tf.conf @@ -9764,7 +9764,7 @@ select = name; EFL-1_L1 "EFL1 L1" = 3211; N2_EFL1_anti-EFL1_L1 "N2 EFL1 anti-EFL1 L1" = 3605; PIE1_EFL1_GFP_YA "EFL1 YA" = 3072; - category = Transcription Factors: GFP ChIP +category = Transcription Factors: GFP ChIP sort_order = name stranded = 0 height = 30 From 530c9c7b4d3e8f9623b9323b41ecc468bc1fd5f4 Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 7 Dec 2015 16:02:53 +0000 Subject: [PATCH 2/2] removed a duplicate track config and fixed the misspelling of "category" which resulted in the track being placed in the "General" category --- waterston_conf/waterston_dev.course.conf | 76 +----------------------- 1 file changed, 1 insertion(+), 75 deletions(-) diff --git a/waterston_conf/waterston_dev.course.conf b/waterston_conf/waterston_dev.course.conf index 7fce969..2d33c37 100644 --- a/waterston_conf/waterston_dev.course.conf +++ b/waterston_conf/waterston_dev.course.conf @@ -7284,7 +7284,7 @@ feature = read_pair glyph = segments data source = 6540 track source = -cateogry = RNA Expression Profiling:mRNA: polyA mRNA reads, developmental timecourse +category = RNA Expression Profiling:mRNA: polyA mRNA reads, developmental timecourse draw_target = 1 show_mismatch = 1 mismatch_color= red @@ -8749,80 +8749,6 @@ mean_color = blue max_color = lightblue height = 20 -[submission_6540.sorted.bam] -database = submission_6540.sorted.bam_bam -feature = read_pair -glyph = segments -data source = 6540 -track source = -cateogry = RNA Expression Profiling:mRNA: polyA mRNA reads, developmental timecourse -draw_target = 1 -show_mismatch = 1 -mismatch_color= red -indel_color = orange -bgcolor = black -fgcolor = black -height = 4 -label = 1 -label_position= left -label density = 50 -link = sub {return "http://intermine.modencode.org/query/portal.do?externalid=modENCODE_6540&class=Submission";} -bump = fast -connector = sub { - my $glyph = pop; - return $glyph->level == 0 ? 'dashed' : 'solid'; - } -maxdepth = 2 -box_subparts = 2 -key = L1LIN35-1cap1 -citation =

- Celegans Dev Timecourse Expression L1LIN35-1cap1 RNA-seq sequences and alignment - (Waterston project, Waterston subgroup) -

-

Details

-

Place a submission-specific statement in here.

-

General Description

-

- Using massively parallel sequencing by synthesis methods, we are surveying transcripts from various stages and strains of the nematode C. elegans. We use novel statistical approaches to evaluate coverage of annotated features of the genome and of candidate processed transcripts. -

-

Protocols

-
    -
  1. - Growth and isolation: - Library preparation for Illumina Sequencing, - Array Capture, - Staging_and_isolation, - RNA_isolation, - Worm_growth -
    2. -
  2. - Sample preparation: - cDNA amplification with random hexamers for sequencing, - Illumina single-end sequencing on GAIIx -
    3. -
  3. - Other Protocols: - Normalization, - Alignment -
    4. -
-
    -
-
    -
  1. - External Links: - SRR137925, - SRR139094 -
    2. -
-
- - -
- Release Date: 2013-11-06 Submission 6540 - [submission_6553.sorted.bam_bam:database] db_adaptor = Bio::DB::Sam db_args = -fasta /browser_data/worm/fasta/c_elegans.WS220.genomic.fa