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Scotts fixes #2

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Scotts fixes #2

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4d72de3
fixing the category for a track (mistake put it in "General" and gave…
scottcain Dec 7, 2015
530c9c7
removed a duplicate track config and fixed the misspelling of "catego…
scottcain Dec 7, 2015
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2 changes: 1 addition & 1 deletion snyder_conf/snyder_gfp_tf.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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76 changes: 1 addition & 75 deletions waterston_conf/waterston_dev.course.conf
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Expand Up @@ -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
Expand Down Expand Up @@ -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 = <h1>
Celegans Dev Timecourse Expression L1LIN35-1cap1 RNA-seq sequences and alignment
(Waterston project, Waterston subgroup)
</h1>
<h2>Details</h2>
<p>Place a submission-specific statement in here.</p>
<h2>General Description</h2>
<p>
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.
</p>
<h2>Protocols</h2>
<ol>
<li>
<b>Growth and isolation:</b>
<a href="http://wiki.modencode.org/project/index.php?title=Library_preparation_for_Illumina_Sequencing:RW:1&oldid=86312">Library preparation for Illumina Sequencing</a>,
<a href="http://wiki.modencode.org/project/index.php?title=Array_Capture:RW:1&oldid=57282">Array Capture</a>,
<a href="http://wiki.modencode.org/project/index.php?title=Worm_staging_and_isolation:RW:Reinke&oldid=82812">Staging_and_isolation</a>,
<a href="http://wiki.modencode.org/project/index.php?title=RNA_isolation:RW:Reinke&oldid=75164">RNA_isolation</a>,
<a href="http://wiki.modencode.org/project/index.php?title=Worm_growth:RW:Reinke&oldid=22843">Worm_growth</a>
</li>
<li>
<b>Sample preparation:</b>
<a href="http://wiki.modencode.org/project/index.php?title=CDNA_amplification_with_random_hexamers_for_sequencing:RW:1&oldid=86308">cDNA amplification with random hexamers for sequencing</a>,
<a href="http://wiki.modencode.org/project/index.php?title=Illumina_single-end_sequencing_on_GAIIx:RW:UW&oldid=84076">Illumina single-end sequencing on GAIIx</a>
</li>
<li>
<b>Other Protocols:</b>
<a href="http://wiki.modencode.org/project/index.php?title=Raw_Coverage_Normalization:RW:1&oldid=75165">Normalization</a>,
<a href="http://wiki.modencode.org/project/index.php?title=RNA_Short_Read_Alignments:RW:Waterston.080901&oldid=81388">Alignment</a>
</li>
</ol>
<ol>
</ol>
<ol>
<li>
<b>External Links:</b>
<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&report=full&term=SRR137925">SRR137925</a>,
<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&report=full&term=SRR139094">SRR139094</a>
</li>
</ol>
<br />
<ul>
</ul>
<ul>
</ul>
<br />
<b>Release Date:</b> 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
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