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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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Serious error in giremi.r #2

Open yuifu opened 8 years ago

yuifu commented 8 years ago

Because several lines in *.Rout have only 23 columns, error occurred at the following code in giremi.r:

dat <- read.table(file=finput,header=T,comment.char="")

Two examples of lines with only 23 columns are as follows:

3    51241928        I       0       Inte    N       N       N       N       0       0       0.000000        -1      -1.000000       -1.000000e+00   0.500000        0       0       0.000000                0       0       0       0

# Corresponding VCF entry
3       51241928        .       A       G       165     PASS    DP=28;VDB=0.248536;SGB=-0.680642;RPB=0.247299;MQB=1;MQSB=1;BQB=0.00241324;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=12,2,10,2;MQ=50    GT:PL:DP:DV:SP:DP4:DPR  0/1:198,0,243:26:12:0:12,2,10,2:14,12
4    61225437        I       0       Inte    A       C       C       N       0       0       0.000000        -1      -1.000000       -1.000000e+00   0.500000        0       0       0.000000                0       0       0       0

# Corresponding VCF entry
4       61225437        .       A       T       17.3338 PASS    DP=17;VDB=0.0279572;SGB=-0.511536;RPB=0.979844;MQB=1;MQSB=1;BQB=0.990991;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=7,6,2,1;MQ=50       GT:PL:DP:DV:SP:DP4:DPR  0/1:52,0,252:16:3:0:7,6,2,1:13,3

Could you guess the cause of this error?

zhqingit commented 8 years ago

Hi Haruka,

Could you send me your SNV list file for test?

Best, Qing

2015-11-22 5:11 GMT-07:00 Haruka Ozaki notifications@github.com:

Because several lines in *.Rout have only 23 columns, error occurred at the following code in giremi.r:

dat <- read.table(file=finput,header=T,comment.char="")

Two examples of lines with only 23 columns are as follows:

3 51241928 I 0 Inte N N N N 0 0 0.000000 -1 -1.000000 -1.000000e+00 0.500000 0 0 0.000000 0 0 0 0

Corresponding VCF entry

3 51241928 . A G 165 PASS DP=28;VDB=0.248536;SGB=-0.680642;RPB=0.247299;MQB=1;MQSB=1;BQB=0.00241324;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=12,2,10,2;MQ=50 GT:PL:DP:DV:SP:DP4:DPR 0/1:198,0,243:26:12:0:12,2,10,2:14,12

4 61225437 I 0 Inte A C C N 0 0 0.000000 -1 -1.000000 -1.000000e+00 0.500000 0 0 0.000000 0 0 0 0

Corresponding VCF entry

4 61225437 . A T 17.3338 PASS DP=17;VDB=0.0279572;SGB=-0.511536;RPB=0.979844;MQB=1;MQSB=1;BQB=0.990991;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=7,6,2,1;MQ=50 GT:PL:DP:DV:SP:DP4:DPR 0/1:52,0,252:16:3:0:7,6,2,1:13,3

Could you guess the cause of this error?

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/2.

yuifu commented 8 years ago

Thanks for your reply, Qing.

I sent you email directory.

Reference geneomes are the mouse genome sequence from the Ensembl (GRCm38.fa).

zhqingit commented 8 years ago

Hi Haruka,

For the intergenic SNVs, the strand should be marked by "#", not "Inte".

Best, Qing

2015-11-23 5:32 GMT-07:00 Haruka Ozaki notifications@github.com:

Thanks for your reply, Qing.

I sent you email directory.

Reference geneomes are the mouse genome sequence from the Ensembl (GRCm38.fa).

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/2#issuecomment-158921280.

yuifu commented 8 years ago

Thank you for your suggestion. However, after I replaced "Inte" with "#" in the 6th column, the same error occurred. Here is the new input file: https://www.dropbox.com/s/k2rbzfg1z7av8mg/test.list.txt?dl=0

zhqingit commented 8 years ago

Hi Haruka,

Could you send me your output file?

Best, Qing

2015-11-24 6:39 GMT-07:00 Haruka Ozaki notifications@github.com:

Thank you for your suggestion. However, after I replaced "Inte" with "#" in the 6th column, the same error occurred. Here is the new input file: https://www.dropbox.com/s/k2rbzfg1z7av8mg/test.list.txt?dl=0

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/2#issuecomment-159269911.

yuifu commented 8 years ago

Thanks, Qing.

Input list: https://www.dropbox.com/s/k2rbzfg1z7av8mg/test.list.txt?dl=0 Output: https://www.dropbox.com/s/nj1qdrvwgzs2374/WT_CT02-1?dl=0

Best regards, Haruka

zhqingit commented 8 years ago

Hi Haruka,

Based on your out file, only site "chr3-81959032" has N, because no reads mapping to this site. I wonder where did you get this SNV list? I also found many sites are the homozygous. Please firstly use some SNVs calling method, such as GATK, to get a set of SNV site.

Best, Qing

2015-11-25 0:06 GMT-07:00 Haruka Ozaki notifications@github.com:

Thanks, Qing.

Input list: https://www.dropbox.com/s/k2rbzfg1z7av8mg/test.list.txt?dl=0 Output: https://www.dropbox.com/s/nj1qdrvwgzs2374/WT_CT02-1?dl=0

Best regards, Haruka

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/2#issuecomment-159521726.