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Old 01-18-2012, 07:02 AM   #1
htchu.taiwan
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Default EBARDenovo - A new RNA-seq do novo assembler for paired-end Illumina data

Hi,

I wrote a program for de novo assembly of paired-end RNA-seq data.

It's a 64-bits Windows command with .Net framework http://msdn.microsoft.com/en-us/library/w0x726c2.aspx.

You can try it on a Windows-7 PC with 16G RAM for the assembly of single run Illumina transcriptomic data (20G, 90bp~100bp paired-end reads).

EBARDenovo is designed for finding lower-expressed transcripts even their coverage depths are very low (even less than 2x).

The download link:
https://sourceforge.net/projects/ebardenovo

I wish you can obtained fine results by my EBARDenovo program.

Best regards,

I am Hsueh-Ting Chu from Taiwan. htchu.taiwan@gmail.com
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Old 04-09-2013, 06:42 AM   #2
figo1019
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Quote:
Originally Posted by htchu.taiwan View Post
Hi,

I wrote a program for de novo assembly of paired-end RNA-seq data.

It's a 64-bits Windows command with .Net framework http://msdn.microsoft.com/en-us/library/w0x726c2.aspx.

You can try it on a Windows-7 PC with 16G RAM for the assembly of single run Illumina transcriptomic data (20G, 90bp~100bp paired-end reads).

EBARDenovo is designed for finding lower-expressed transcripts even their coverage depths are very low (even less than 2x).

The download link:
https://sourceforge.net/projects/ebardenovo

I wish you can obtained fine results by my EBARDenovo program.

Best regards,

I am Hsueh-Ting Chu from Taiwan. htchu.taiwan@gmail.com
Hi Hsueh-Ting Chu

I tried to run the EBARDenovo with the example files provided in the sample. It works fine, but when I try to run my sequences I am getting the error. I am copying the log file output. Can you tell me what can be the reason for this error and how I can correct it.
"Step 1: Build indices ...04/09 12:31:43
Scan reads (Bulks of 100000 spots) ...
The paired reads have different lengths:94,32 bps
The bigger reads are to be trimmed from 94 to 32 bps
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 7
2 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 13
0 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181
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 2
84 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 33
5 336 337 338 339 340 341 342 Fin
Build indx (Bulks of 100000 spots) ...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 1
72 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 22
3 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274
275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325
326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 Fin
Step 2: Save indices ...(skipped)
Step 3: Assembly ...04/09 12:59:22

Unhandled Exception:
System.ArgumentOutOfRangeException: Argument is out of range.
Parameter name: startIndex
at System.String.Substring (Int32 startIndex) [0x00000] in <filename unknown>:0
at BioAsia.EbarDenovo.EbarContig.RepeatSensingRight () [0x00000] in <filename unknown>:0
at BioAsia.EbarDenovo.EbarAssembly.AcrossInsertOne (System.Collections.Generic.Queue`1 queueIsoContig) [0x00000] in <filename unknown>:0
at BioAsia.EbarDenovo.EbarAssembly.AcrossInsert (BioAsia.EbarDenovo.EbarContig contigNew) [0x00000] in <filename unknown>:0
at BioAsia.EbarDenovo.EbarAssembly.SRun (System.Object stateInfo) [0x00000] in <filename unknown>:0
"
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Old 04-09-2013, 06:05 PM   #3
frozenlyse
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Bioinformatics..... on Windows?

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Old 04-14-2013, 04:25 PM   #4
elzed
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I think Hsueh-Ting forgot to mention that you can use the software with 'mono EBARDenovo' on Unix.
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Old 04-15-2013, 03:34 AM   #5
kopi-o
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The problem is that it doesn't work ... At least it didn't for me. When I encountered a crash in mono, I emailed Hsueh-Ting and got the following reply:

Quote:
Although Mono.Net let .net programs be run on Linux, Mono is not 100% compatable with Microsoft .NET.
Mono.Net will meet problems on massive memory operations.
As a result, I suggest you can try to run EBARDenovo on Windows.
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Old 04-15-2013, 03:46 AM   #6
NicoBxl
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Unfortunately all big computing grid work on a unix-based system..and so this tool is born dead...
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Old 04-15-2013, 04:16 PM   #7
elzed
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Quote:
Originally Posted by kopi-o View Post
The problem is that it doesn't work ... At least it didn't for me. When I encountered a crash in mono, I emailed Hsueh-Ting and got the following reply:
My Unix is 'x86_64 x86_64 x86_64 GNU/Linux'.

I tried it with supplied samples data.

It worked out. I have not tried any real world data.

What's your system? is it _64 system?
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Old 04-15-2013, 07:51 PM   #8
snetmcom
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Quote:
Originally Posted by NicoBxl View Post
Unfortunately all big computing grid work on a unix-based system..and so this tool is born dead...
You don't need grid's for all assemblies. Hardware is also not really tied to software.
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Old 04-15-2013, 08:05 PM   #9
Cofactor Genomics
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Have you stepped it through its paces yet?
ie compared it to other transcriptome assemblers in context of a RNA-seq set against well characterized gene models?
Will it only take ILMN reads, or will it also use 454 (we commonly use both in our transcriptome assembly approaches and it really helps refine our gene models).


Jarret Glasscock
Cofactor Genomics
http://www.cofactorgenomics.com
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Old 04-16-2013, 12:08 AM   #10
kopi-o
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Quote:
It worked out. I have not tried any real world data.

What's your system? is it _64 system?
Yes, it's a standard x86_64 Linux cluster, where I have previously used mono to run Fusionmap successfully. The provided samples are probably quite small and not representative of the data sets you would use. As the author indicated in the mail to me, it seems mono struggles with "massive memory operations".
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