-
Notifications
You must be signed in to change notification settings - Fork 0
/
fileds.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 84 should actually have 1 column, instead of 2 in line 83.
313 lines (313 loc) · 7.06 KB
/
fileds.csv
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
Sample Name
Lane
BarcodeIdx
Project
Harvest By
Harvest Date
Harvest Time
First Strand Amp By
First Strand Amp Date
Amplified By
Amplified Date
Library By
Library Date
Species
Strain
Strain Other
Age Harvested Unit
Age Harvested Unit Other
Age Harvested Value
Age Culture
Harvest Method
Harvest Quant
Harvest Compound
Is Harvest Compound Uncaged
Region
Subregion
Subregion Other
Cell Class
Cell Class Other
Cell Type
Cell Type Other
Supplier
Source Type
Source Unit
Source Unit Other
Source Region
Source Region Other
Patient ID
Cell ID
Dendrite ID
Source Well ID
Treatment
Replicate
Source Amplification Method
Source Amplification Rounds
First Sequencing Barcode
Second Sequencing Barcode
Non-Sequencing Barcode
Spike-In Type
Spike-In Dilution
Library Input Amount
Library Kit
Strand Specific
Library Const PCR Cycles
Amplification Protocol
Library Protocol
Analysis Protocol
Contaminants File
dbGaP Release
SRA ID
Notes
pipeline
STAR.star.version
STAR.samtools.version
STAR.species (genome)
STAR.SE
STAR.readLength
STAR.Tot Reads After Trim
STAR.Avg Inp Read Len
STAR.Avg Uniq Map Len
STAR.Perc Bases Mismatched
STAR.Uniq-mapped Reads
STAR.Total-mapped Reads
STAR.Uniq-mapped Perc
STAR.Multi-mapped Perc
STAR.Not-mapped Perc
VERSE.verse.version
VERSE.transcriptome
VERSE.stranded
VERSE.ID_attribute
VERSE.introns
VERSE.intergenic
VERSE.lines-sines
VERSE.exons Level 1,2: non-SpikeIn Reads Counted
VERSE.exons Level 1,2: SpikeIn ReadsCounted
VERSE.exons Level 1,2: Num Genes
VERSE.exons Level 1,2: Avg Read Per Gene
VERSE.exons Level 1,2: Max Reads Per Gene
VERSE.exons Level 1,2: Ambiguous Mapped
VERSE.exons Level 3: Reads Counted
VERSE.exons Level 3: Num Genes
VERSE.exons Level 3: Avg Read Per Gene
VERSE.exons Level 3: Max Reads Per Gene
VERSE.exons Level 3: Ambiguous Mapped
VERSE.anti-exons: non-spikeIn Reads Counted
VERSE.anti-exons: spikeIn Reads Counted
VERSE.anti-exons: Reads Counted
VERSE.anti-exons: Num Genes
VERSE.anti-exons: Avg Read Per Gene
VERSE.anti-exons: Max Reads Per Gene
VERSE.anti-exons: Ambiguous Mapped
VERSE.introns Level 1,2: Reads Counted
VERSE.introns Level 1,2: Num Genes
VERSE.introns Level 1,2: Avg Read Per Gene
VERSE.introns Level 1,2: Max Reads Per Gene
VERSE.introns Level 1,2: Ambiguous Mapped
VERSE.introns Level 3: Reads Counted
VERSE.introns Level 3: Num Genes
VERSE.introns Level 3: Avg Read Per Gene
VERSE.introns Level 3: Max Reads Per Gene
VERSE.introns Level 3: Ambiguous Mapped
VERSE.anti-introns: Reads Counted
VERSE.anti-introns: Num Genes
VERSE.anti-introns: Avg Read Per Gene
VERSE.anti-introns: Max Reads Per Gene
VERSE.anti-introns: Ambiguous Mapped
VERSE.mito: Reads Counted
VERSE.mito: Num Genes
VERSE.mito: Avg Read Per Gene
VERSE.mito: Max Reads Per Gene
VERSE.mito: Ambiguous Mapped
VERSE.anti-mito: Reads Counted
VERSE.anti-mito: Num Genes
VERSE.anti-mito: Avg Read Per Gene
VERSE.anti-mito: Max Reads Per Gene
VERSE.anti-mito: Ambiguous Mapped
VERSE.Intergenic: Reads Counted
VERSE.Intergenic: Num Regions
VERSE.Intergenic: Avg Read Per Region
VERSE.Intergenic: Max Reads Per Region
VERSE.Intergenic: Ambiguous Mapped
VERSE.LINE Reads
VERSE.SINE Reads
VERSE.Num LINEs
VERSE.Num SINEs
VERSE.Neither LINEs nor SINEs
VERSE.No Feature
VERSE.Reads Missing Mates
VERSE.Perc: Exons Level 1,2
VERSE.Perc: Exons Level 3
VERSE.Perc: Anti-Exons
VERSE.Perc: Introns Level 1,2
VERSE.Perc: Introns Level 3
VERSE.Perc: Anti-Introns
VERSE.Perc: Mito
VERSE.Perc: Anti-Mito
VERSE.Perc: Intergenic
VERSE.Perc: Spike-In
BLAST.blastn.version
BLAST.parseBlast.py.version
BLAST.species
BLAST.readLength
BLAST.numReads
BLAST.kmer
BLAST.Total Hits
BLAST.Hits Not Counted
BLAST.Perc Hits Not Target or SpikeIn
BLAST.Bacteria
BLAST.Danio
BLAST.Fly
BLAST.Human
BLAST.Mouse
BLAST.Rat
BLAST.Yeast
BLAST.Carp
BLAST.ERCC
BLAST.PhiX
BLAST.TATAGTGAGT
BLAST.Perc Counted
TRIM.trimReads.py.version
TRIM.minLen
TRIM.phredThresh
TRIM.removeN
TRIM.numAT
TRIM.SE
TRIM.ContamFile
TRIM.nTotalReadsBeforeTrim
TRIM.nBothTrimmed
TRIM.nFirstTrimmed
TRIM.nSecondTrimmed
TRIM.nBothDiscarded
TRIM.nFirstDiscarded
TRIM.nSecondDiscarded
TRIM.Phred Threshold (first)
TRIM.Phred Threshold (second)
TRIM.removed5N (first)
TRIM.removed5N (second)
TRIM.removed3N (first)
TRIM.removed3N (second)
TRIM.init3G (first)
TRIM.init3G (second)
TRIM.indexAdapter (first)
TRIM.indexAdapter (second)
TRIM.univAdapterRC (first)
TRIM.univAdapterRC (second)
TRIM.aRNAPrimer (first)
TRIM.aRNAPrimer (second)
TRIM.aRNAPrimerRC (first)
TRIM.aRNAPrimerRC (second)
TRIM.tivaXoligo (first)
TRIM.tivaXoligo (second)
TRIM.tivaXoligoRC (first)
TRIM.tivaXoligoRC (second)
TRIM.dT5oligo (first)
TRIM.dT5oligo (second)
TRIM.dT5oligoRC (first)
TRIM.dT5oligoRC (second)
TRIM.dT6oligo (first)
TRIM.dT6oligo (second)
TRIM.dT6oligoRC (first)
TRIM.dT6oligoRC (second)
TRIM.NexteraRead1ExternalAdapter (first)
TRIM.NexteraRead1ExternalAdapter (second)
TRIM.NexteraRead2ExternalAdapter (first)
TRIM.NexteraRead2ExternalAdapter (second)
TRIM.ChexPolyCprimerRC (first)
TRIM.ChexPolyCprimerRC (second)
TRIM.istT7primerRC (first)
TRIM.istT7primerRC (second)
TRIM.NexteraTransposaseAdapterR1 (first)
TRIM.NexteraTransposaseAdapterR1 (second)
TRIM.NexteraTransposaseAdapterR1RC (first)
TRIM.NexteraTransposaseAdapterR1RC (second)
TRIM.NexteraTransposaseAdapterR2 (first)
TRIM.NexteraTransposaseAdapterR2 (second)
TRIM.NexteraTransposaseAdapterR2RC (first)
TRIM.NexteraTransposaseAdapterR2RC (second)
TRIM.NexteraTransposonEndSequence (first)
TRIM.NexteraTransposonEndSequence (second)
TRIM.NexteraTransposonEndSequenceRC (first)
TRIM.NexteraTransposonEndSequenceRC (second)
TRIM.SmartSeqTSO (first)
TRIM.SmartSeqTSO (second)
TRIM.SmartSeqTSORC (first)
TRIM.SmartSeqTSORC (second)
TRIM.SmartSeqOligo (first)
TRIM.SmartSeqOligo (second)
TRIM.SmartSeqOligoRC (first)
TRIM.SmartSeqOligoRC (second)
TRIM.5 polyT (first)
TRIM.5 polyT (second)
TRIM.3 polyA (first)
TRIM.3 polyA (second)
TRIM.removed5A (first)
TRIM.removed5A (second)
TRIM.removed3A (first)
TRIM.removed3A (second)
TRIM.removed5T (first)
TRIM.removed5T (second)
TRIM.removed3T (first)
TRIM.removed3T (second)
TRIM.removed5C (first)
TRIM.removed5C (second)
TRIM.removed3C (first)
TRIM.removed3C (second)
TRIM.removed5G (first)
TRIM.removed5G (second)
TRIM.removed3G (first)
TRIM.removed3G (second)
RMDUP.removeDuplicates.py.version
RMDUP.nInitialReadPairs
RMDUP.nUniqueReadPairs
RMDUP.nDuplicatesFound
RMDUP.nReadsWithDuplicates
RMDUP.maxDuplicateCount
GMAP.gmap.version
GMAP.samtools.version
GMAP.species (genome)
GMAP.SE
GMAP.readLength
GMAP.Reads After Trim
GMAP.Reads Mapped
GMAP.Uniq Reads
GMAP.Mismatches
GMAP.Bases Mapped
GMAP.Avg Read Length
GMAP.Max Read Length
BARCODE.kmerFind.py.version
BARCODE.barcode
BARCODE.prefix
BARCODE.suffix
BARCODE.cut
BARCODE.SE
BARCODE.R1_threshold
BARCODE.R2_threshold
BARCODE.nTotalReadsBeforeMapping
BARCODE.totalBothMapped
BARCODE.totalFirstMapped
BARCODE.totalSecondMapped
BARCODE.firstKmer
BARCODE.firstRC
BARCODE.secondKmer
BARCODE.secondRC
BARCODE.avgPosFirst
BARCODE.avgPosSecond
BARCODE.avgPosFirstForward
BARCODE.avgPosFirstReverse
BARCODE.avgPosSecondForward
BARCODE.avgPosSecondReverse
Experiment Name
Description
Investigators
External Lab
Submitted Date
Machine Manufacturer
Model
Sequencing Kit
Read Length
Paired
Facility
Facility ID
Processing
Notes