error:Can't find snv in ss!i

[jingyayeah]

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]

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]

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]

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