Can any one share a quick guide on how to install and run BFAST for SOLiD data? The book does not give a clear instruction so does the readme file. If we do target resequencing, not the complete genome rather genes how should the reference file be prepared. Thanks much in advance.
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Originally posted by jsun529 View PostCan any one share a quick guide on how to install and run BFAST for SOLiD data? The book does not give a clear instruction so does the readme file. If we do target resequencing, not the complete genome rather genes how should the reference file be prepared. Thanks much in advance.
The easiest way to run BFAST in a "targetted" mode is to create indexes that only use the targetted regions. This can be accomplished using the "-x" option in when running "bfast index". Example input files can be found in the manual.
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So, the bfast-book or the readme did not say how to install the program, also for the ABI solid example section 7.1.2, for the bpreprocess or bmatches, could not find any of this command from the source code downloaded through sourceforge for the latest version?.
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on the INSTALL page it said refer to the man pages for documentation
doc/bpreprocess.1
but where is this doc folder, this is really confusing and not user friendly and it would be better everything are in one place, say the bfast book or something.
Thanks,
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I have the preprocess running however i got this error message when I trying to create the indexes, any one know how to fix this? Thanks.(I have fragment data not mate pair)
bfast-0.5.6/bpreprocess/bpreprocess -r bfast.rg.file.OPA1.1.brg -i layouts.txt -a 1 -A 1 -o OPA1 -d ./ -T ./
************************************************************
Checking input parameters supplied by the user ...
Validating rgFileName bfast.rg.file.OPA1.1.brg.
Validating indexLayoutFileName layouts.txt.
Validating exonsFileName Default.txt.
Validating outputID OPA1.
Validating outputDir ./.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: 1 [ExecuteProgram]
rgFileName: bfast.rg.file.OPA1.1.brg
algorithm: 1
space: 1
indexLayoutFileName: layouts.txt
repeatMasker: 0
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: Default.txt
numThreads: 1
outputID: OPA1
outputDir: ./
tmpDir: ./
timing: 0
************************************************************
************************************************************
Reading in reference genome from bfast.rg.file.OPA1.1.brg.
In total read 1 contigs for a total of 104204 bases
************************************************************
************************************************************
In function "RGIndexLayoutRead": Fatal Error[OpenFileError]. Message: Could not open index layout file reading.
***** Exiting due to errors *****
************************************************************
Comment
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Originally posted by jsun529 View PostI have the preprocess running however i got this error message when I trying to create the indexes, any one know how to fix this? Thanks.(I have fragment data not mate pair)
bfast-0.5.6/bpreprocess/bpreprocess -r bfast.rg.file.OPA1.1.brg -i layouts.txt -a 1 -A 1 -o OPA1 -d ./ -T ./
************************************************************
Checking input parameters supplied by the user ...
Validating rgFileName bfast.rg.file.OPA1.1.brg.
Validating indexLayoutFileName layouts.txt.
Validating exonsFileName Default.txt.
Validating outputID OPA1.
Validating outputDir ./.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: 1 [ExecuteProgram]
rgFileName: bfast.rg.file.OPA1.1.brg
algorithm: 1
space: 1
indexLayoutFileName: layouts.txt
repeatMasker: 0
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: Default.txt
numThreads: 1
outputID: OPA1
outputDir: ./
tmpDir: ./
timing: 0
************************************************************
************************************************************
Reading in reference genome from bfast.rg.file.OPA1.1.brg.
In total read 1 contigs for a total of 104204 bases
************************************************************
************************************************************
In function "RGIndexLayoutRead": Fatal Error[OpenFileError]. Message: Could not open index layout file reading.
***** Exiting due to errors *****
************************************************************
I would suggests upgrading to the 0.6.0 version as the user interface has been improved.
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Ok, when running the bmatches I got this error message using the example settings.
sudo bfast-0.5.6/bmatches/bmatches -r bfast.rg.file.OPA1.1.brg -i main.indexes.txt -I secondary.indexes.txt -R OPA1F3.1.fastq -O offsets.txt -A 1 -K 8 -M 384 -o OPA1.1 -d ./ -T ./
************************************************************
Checking input parameters supplied by the user ...
Validating rgFileName bfast.rg.file.OPA1.1.brg.
Validating bfastMainIndexesFileName main.indexes.txt.
Validating bfastSecondaryIndexesFileName secondary.indexes.txt.
Validating readsFileName OPA1F3.1.fastq.
Validating offsetsFileName offsets.txt.
Validating outputID OPA1.1.
Validating outputDir ./.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: 1 [ExecuteProgram]
rgFileName: bfast.rg.file.OPA1.1.brg
bfastMainIndexesFileName main.indexes.txt
bfastSecondaryIndexesFileName secondary.indexes.txt
readsFileName: OPA1F3.1.fastq
offsetsFileName: offsets.txt
space: 1
startReadNum: -1
endReadNum: -1
keySize: 0
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: 0 [BothStrands]
numThreads: 1
queueLength: 100000
outputID: OPA1.1
outputDir: ./
tmpDir: ./
timing: 0
************************************************************
************************************************************
Reading in reference genome from bfast.rg.file.OPA1.1.brg.
In total read 1 contigs for a total of 104204 bases
************************************************************
Reading OPA1F3.1.fastq into temp files.
Will process 1933855 reads.
************************************************************
Will output to ./bfast.matches.file.OPA1.1.bmf.
************************************************************
Processing 1933855 reads using 20 main indexes.
************************************************************
Searching index 1 out of 20...
Reading index from 14.
************************************************************
In function "RGIndexRead": Fatal Error[OpenFileError]. Variable/Value: 14.
Message: Could not open rgIndexFileName for reading.
***** Exiting due to errors *****
************************************************************
any suggestions? Thanks,
Comment
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Originally posted by jsun529 View PostOk, when running the bmatches I got this error message using the example settings.
sudo bfast-0.5.6/bmatches/bmatches -r bfast.rg.file.OPA1.1.brg -i main.indexes.txt -I secondary.indexes.txt -R OPA1F3.1.fastq -O offsets.txt -A 1 -K 8 -M 384 -o OPA1.1 -d ./ -T ./
************************************************************
Checking input parameters supplied by the user ...
Validating rgFileName bfast.rg.file.OPA1.1.brg.
Validating bfastMainIndexesFileName main.indexes.txt.
Validating bfastSecondaryIndexesFileName secondary.indexes.txt.
Validating readsFileName OPA1F3.1.fastq.
Validating offsetsFileName offsets.txt.
Validating outputID OPA1.1.
Validating outputDir ./.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: 1 [ExecuteProgram]
rgFileName: bfast.rg.file.OPA1.1.brg
bfastMainIndexesFileName main.indexes.txt
bfastSecondaryIndexesFileName secondary.indexes.txt
readsFileName: OPA1F3.1.fastq
offsetsFileName: offsets.txt
space: 1
startReadNum: -1
endReadNum: -1
keySize: 0
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: 0 [BothStrands]
numThreads: 1
queueLength: 100000
outputID: OPA1.1
outputDir: ./
tmpDir: ./
timing: 0
************************************************************
************************************************************
Reading in reference genome from bfast.rg.file.OPA1.1.brg.
In total read 1 contigs for a total of 104204 bases
************************************************************
Reading OPA1F3.1.fastq into temp files.
Will process 1933855 reads.
************************************************************
Will output to ./bfast.matches.file.OPA1.1.bmf.
************************************************************
Processing 1933855 reads using 20 main indexes.
************************************************************
Searching index 1 out of 20...
Reading index from 14.
************************************************************
In function "RGIndexRead": Fatal Error[OpenFileError]. Variable/Value: 14.
Message: Could not open rgIndexFileName for reading.
***** Exiting due to errors *****
************************************************************
any suggestions? Thanks,
1. I would recommend using all possible offsets.
2. Long gaps 60bp will be difficult to detect with short reads directly.
3. It looks like the "main.indexes.txt" file is incorrectly formatted. It should just be file paths.
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Thanks. This will be my last question for the test run I think :-)
when I do this bpostprocess as recommended by the book I got these error message as
ocalhost:~/Desktop/OPA1.BFAST # bfast-0.5.6/bpostprocess/bpostprocess -i bfast.aligned.file.OPA1.baf -r bfast.rg.file.OPA1.0.brg -a 3 -o OPA1 -d ./ -O 3
************************************************************
Checking input parameters supplied by the user ...
Validating rgFileName bfast.rg.file.OPA1.0.brg.
Validating alignFileName bfast.aligned.file.OPA1.baf.
Validating outputID OPA1.
Validating outputDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: 1 [ExecuteProgram]
rgFileName: bfast.rg.file.OPA1.0.brg
alignFileName: bfast.aligned.file.OPA1.baf
algorithm: 3 [Best Score]
queueLength: 10000
outputID: OPA1
outputDir: ./
outputFormat: 6
timing: 0
************************************************************
************************************************************
Reading in reference genome from bfast.rg.file.OPA1.0.brg.
In total read 1 contigs for a total of 104204 bases
************************************************************
Processing reads, currently on:
0************************************************************
In function "ConvertReadFromColorSpace": Fatal Error[OutOfRange]. Variable/Value: read.
Message: Could not convert base and color.
***** Exiting due to errors *****
************************************************************
not sure which part cause this? Thanks
Comment
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Originally posted by jsun529 View PostThanks. This will be my last question for the test run I think :-)
when I do this bpostprocess as recommended by the book I got these error message as
ocalhost:~/Desktop/OPA1.BFAST # bfast-0.5.6/bpostprocess/bpostprocess -i bfast.aligned.file.OPA1.baf -r bfast.rg.file.OPA1.0.brg -a 3 -o OPA1 -d ./ -O 3
************************************************************
Checking input parameters supplied by the user ...
Validating rgFileName bfast.rg.file.OPA1.0.brg.
Validating alignFileName bfast.aligned.file.OPA1.baf.
Validating outputID OPA1.
Validating outputDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: 1 [ExecuteProgram]
rgFileName: bfast.rg.file.OPA1.0.brg
alignFileName: bfast.aligned.file.OPA1.baf
algorithm: 3 [Best Score]
queueLength: 10000
outputID: OPA1
outputDir: ./
outputFormat: 6
timing: 0
************************************************************
************************************************************
Reading in reference genome from bfast.rg.file.OPA1.0.brg.
In total read 1 contigs for a total of 104204 bases
************************************************************
Processing reads, currently on:
0************************************************************
In function "ConvertReadFromColorSpace": Fatal Error[OutOfRange]. Variable/Value: read.
Message: Could not convert base and color.
***** Exiting due to errors *****
************************************************************
not sure which part cause this? Thanks
Comment
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when i use samtools.pl varFilter to filter the variant and snps, it seemed the program have a cap on the maximum read depth, it filtered most of the candidates that has higher coverage that should not be filtered, however when I try to redefine the D through command line arg, the program return nothing after filtering, any one know how to fix it?
Thanks
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