Phred+64 refers to old format illumina (v.1.3+) quality calls. If you have recent data then it is going to be in Phred+33 (Sanger) format. See: http://en.wikipedia.org/wiki/FASTQ_format
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thanks. So if you have RNAseq data from an Hiseq 2500 then you should specify Phred+33 in tophat?Comment
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That is the default.Comment
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great, thanks again!
gComment
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I exceuted the tophat to align against the reference genome. I found the following files:
1. accepted_hits.bam
2. unmapped.bam
3.junction.bed
4. align.txt
here accepted_hits.bam, size is 1 KB while unmapped.bam has 200MB. Align.txt shows :
Reads:
Input : 528840
Mapped : 0 ( 0.0% of input)
0.0% overall read mapping rate.
Please help me to define the parameters to align and mapped against the heterologous genomes.Comment
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I download the data from Ensembl. Is it any problem in it.
I exceuted the tophat to align against the reference genome. I found the following files:
1. accepted_hits.bam
2. unmapped.bam
3.junction.bed
4. align.txt
here accepted_hits.bam, size is 1 KB while unmapped.bam has 200MB. Align.txt shows :
Reads:
Input : 528840
Mapped : 0 ( 0.0% of input)
0.0% overall read mapping rate.
Please help me to define the parameters to align and mapped against the heterologous genomes.Comment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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