zhqingit
commented
8 years ago Hi,
I guess you didn't do any filtering for your SNV calling. So please only keep the heterogeneous SNVs after removing the sequencing errors.
Best, Qing
2016-05-23 18:24 GMT-07:00 HungerNature notifications@github.com:
Dear All, I had try to use giremi to run on my RNA-seq datasets, two weeks ago I begun to run it. But it still run until now. Did I make some problems? Fllowing is my excute command line: ~/software/giremi/giremi -f /path/to/genome.fa -l /home/database/GRCh38/SNPs.giremi.txt -o sample.res sample.sorted.bam > sample.giremi.run.log 2>&1 &
The bam file was used hisat2 software to mapping with index download from hisat2 software websites. We have four bam file to run, the file size from 2.0G to 12.0G. But all of them didn't finish yet. The SNPs.giremi.txt got from dbSNPs, and make it to fit giremi. And it has 61351128 lines. Its head lines look like: 1 10642 10643 R5 1 + 1 11008 11009 R5 1 + 1 11012 11013 R5 1 + 1 11063 11064 R5 1 + 1 13110 13111 INT 1 + 1 13116 13117 INT 1 + 1 13273 13274 ASP 1 + 1 13284 13285 ASP 1 + 1 13380 13381 ASP 1 + 1 13445 13446 ASP 1 + Any suggestions and comments are welcome! Thank you for your kindness!
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Dear All, I had try to use giremi to run on my RNA-seq datasets, two weeks ago I begun to run it. But it still run until now. Did I make some problems? Fllowing is my excute command line: ~/software/giremi/giremi -f /path/to/genome.fa -l /home/database/GRCh38/SNPs.giremi.txt -o sample.res sample.sorted.bam > sample.giremi.run.log 2>&1 &
The bam file was used hisat2 software to mapping with index download from hisat2 software websites. We have four bam file to run, the file size from 2.0G to 12.0G. But all of them didn't finish yet. The SNPs.giremi.txt got from dbSNPs, and make it to fit giremi. And it has 61351128 lines. Its head lines look like: 1 10642 10643 R5 1 + 1 11008 11009 R5 1 + 1 11012 11013 R5 1 + 1 11063 11064 R5 1 + 1 13110 13111 INT 1 + 1 13116 13117 INT 1 + 1 13273 13274 ASP 1 + 1 13284 13285 ASP 1 + 1 13380 13381 ASP 1 + 1 13445 13446 ASP 1 + Any suggestions and comments are welcome! Thank you for your kindness!