Hi
I'm starting to use bfast and I have some doubts about some indexing parameters.
When indexing do I have to do it with the...
50 results in 0.0031 seconds.
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bfast match "hangs" while reading index
When I run bfast match (version 0.7.0a), the program often "hangs" while reading the index (as evidenced by the last line of output to stderr):... -
BFAST, Could not read in buffer
I'm having some problem getting started with Bfast:
bob@homequad:/home2/NGS/tmp$ bfast index -n 8 -f /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta... -
BFAST easyalign default
Hi,
I was wondering what the defaults for BFAST postprocess command for paired end SOLiD reads are? With the -p command, it gives
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SOLiD csfasta to fastq using BFAST+BWA
Hi,
I'm trying to convert my SOLiD reads to FASTQ using BFAST+BWA's solid2fastq.pl utility. I have two sets of paired-end files
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BFAST match error
Hi,
I'm getting the following error from BFAST with my colorspace SOLiD reads in FASTQ format. Couldn't figure out what it is...
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what does these mean?
Recently I'm using BFAST to do some alignments.
In the output SAM file there are many columns. After reading the document of SAM, I still have a... -
BFast match and preprocess questions
Hi,
I am trying to map solid reads using bfast, and have several questions on using it, any help will be highly appreciated!
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Is trimming necessary before mapping SOLiD data with BFAST?
Hi,
I am wondering whether trimming is necessary if using BFAST for aligning SOLiD reads? BFAST has been pretty powerful in mapping cs...Last edited by sonia.bao; 06-01-2012, 09:21 PM. -
Scaling Bfast MQ to BWA MQ
I am using Bfast to align SOLiD reads and BWA for illumina reads. I am calling SNPs and Indels using GATK, combining SOLiD and Illumina data.
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SOLiD paired-end read analysis with BFAST 0.7.0a
I am trying to get going with paired-end mapping using BFAST 0.7.0a, but stalling so far.
I have 50bp F3 reads and 35bp F5-BC reads from... -
BFAST scoring matrix
Hello folks,
I wonder what the default scoring matrix is in BFAST. I can only find information on instructions of how to set one, but there... -
error during GATK indel realigner
Hello,
I've performed an exome alignement (paired end reads) by using bfast match + localalign + postprocess, thereafter I've removed duplicates... -
how to merge paired ends provided in separate files during (bfast) alignement
Hello,
I want to align illumina paired-end reads by using bfast. The point is that each end is provided in two separate .fastq files. ... -
which human Reference genome to use
I guess it is a very stupid question, but there is a difference between using the hg19 reference genome vs the GRCh37?
I want to align...
