Hi! I mapped RNA-seq of Synechococcus sp PCC7002 and used this code:
bowtie -p 2 -C -S SynechococcusPCC7002 SRR308187.fastq > $SRR308187.sam...
17 results in 0.0023 seconds.
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Uniquely mapped reads on Bowtie with colorspace RNA-seq
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Colorspace bis-seq data analysis on Solid
What is your recommendation for analyzing bisulphit data? There are very few tools with various output (generally non human readable) and performance... -
Tophat and colorspace error #Solid #csfasta #length of quality string does not match
Hi All,
A lot of people have asked this but there seems to be no resolution on this so far. I am getting this error and after going through... -
Tophat colorspace problem --integer-quals 0
Hello everyone,
Is there an tophat option for setting the --integer-quals to 0 when using colorspace reads? I have a fastq file with phred33... -
bowtie-0.12.7 paired-end colorspace quality bigger than 4.0
Some times in colorspace mode bowtie reports quality values bigger than 4.0
Since, I think, this corresponds to probabilities bigger than 1... -
1000genomes SRR107002.filt.fastq.gz bad format?
The first few lines of ftp://ftp.1000genomes.ebi.ac.uk/vol1....filt.fastq.gz are:
@SRR010375.1 VAB_S0083_BCM_20080731_1_Pilot_2_YRI_Fragment2199_1705_1499... -
Tophat colorspace problem
Hello everyone,
I'm trying to get tophat work with csfasta and qual files.
My command is now:
tophat2 -G ../GENOMES/human_GRCh37_gatk/GRCh37_genes_nochr.gtf... -
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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Mapping SOLiD colorspace paired end reads
Hi, I'm trying to get a sense of what the current consensus is regarding the best practice for mapping SOLiD colour-space paired-end reads. As far as... -
SRMA - Error - cs TAG
Hi,
First time using SRMA, followed the user guide on source forge. Left all variables as defaults. It came up with this error. Any suggestions... -
Mapping of SOLiD reads
Hi. I have a small question about mapping small SOLiD reads against a reference library of small sequences. I'm using Bowtie at the moment and i notice... -
Does bwa support SOLiD PE data?
Hi,
I have used 'bwa aln' and 'bwa sampe' for mapping Exome captured SOLiD PE reads.
I am getting very low PE mapping % (29-35%) One of... -
bs-seq in colorspace
there is some discussion of this in another thread.
i'm considering doing the following for bs-treated reads in colorspace:
... -
how do I output the CS tag for BWA align of SOLID reads?
Hi,
I am trying to use GATK to run some analysis on BWA aligned colorspace reads but I encountered this problem described here
http://g... -
ABI SOLiD data filtering and conversion to base-space
I have previously been using Solexa for small RNA sequencing but am trying out SOLiD. I just received the data back for my first SOLiD smallRNA sequencing...
