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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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error:Can't find snv in ss!i #19

Open jingyayeah opened 8 years ago

jingyayeah commented 8 years ago

command: giremi -f Zea_mays.B73_RefGen_v2.genome.fa -l Input_for_RNA_edit.txt -o out.res accepted_hits.bam

Error: [mpileup] 1 samples in 1 input files error:Can't find snv in ss!i

head Input_for_RNA_edit.txt

chr1 6742 6743 GRMZM5G888250 1 - chr1 6748 6749 GRMZM5G888250 1 - chr1 6849 6850 GRMZM5G888250 1 - chr1 6890 6891 GRMZM5G888250 1 - chr1 6983 6984 GRMZM5G888250 1 - chr1 7034 7035 GRMZM5G888250 1 - chr1 7079 7080 GRMZM5G888250 1 - chr1 7796 7797 GRMZM5G888250 1 - chr1 8995 8996 GRMZM5G888250 1 - chr1 9098 9099 GRMZM5G888250 1 -

zhqingit commented 8 years ago

Hi,

I guess some reads in your bam/sam file might map to multiple positions.

Best, Qing

2016-06-07 1:37 GMT-07:00 jingyayeah notifications@github.com:

command: giremi -f Zea_mays.B73_RefGen_v2.genome.fa -l Input_for_RNA_edit.txt -o out.res accepted_hits.bam

Error: [mpileup] 1 samples in 1 input files error:Can't find snv in ss!i

head Input_for_RNA_edit.txt

chr1 6742 6743 GRMZM5G888250 1 - chr1 6748 6749 GRMZM5G888250 1 - chr1 6849 6850 GRMZM5G888250 1 - chr1 6890 6891 GRMZM5G888250 1 - chr1 6983 6984 GRMZM5G888250 1 - chr1 7034 7035 GRMZM5G888250 1 - chr1 7079 7080 GRMZM5G888250 1 - chr1 7796 7797 GRMZM5G888250 1 - chr1 8995 8996 GRMZM5G888250 1 - chr1 9098 9099 GRMZM5G888250 1 -

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jingyayeah commented 8 years ago

Hi，Qing I have some questions about mapping. Following the article,the unbiased mapping is mapping each end of the paired-end reads to the genome and a dual-filtering scheme is used，so my questions is：

  1. Blat result do not include informations about mismatch position , how to used if for filtering?
  2. Which bam file is used as the input of giremi? (Bowtie ? but there are 4 bam files from 1 sample)

Best, Wang

jingyayeah commented 8 years ago

Hi,Qing

I get the same problem when my bam/sam file filter out multiple positions. (Because I use the bam file with another snv list successful )

Is there some other reasons ?

Best,

Wang