repeat snv and cannot find the ifRNAE

[hemingwang]

Hi Qing, I have some problems when I use the giremi. The first is the "repeat snv".When I annotated the variations, some point be annotated to 2 more genes.The 2 point are the same position,but the gene is different. For example, chr1 15664086 15664087 DDI2 0 + chr1 15664086 15664087 RSC1A1 0 + so how do I deal with this problem? Another question is I cannot computed the ifRNAE. I am looking forward to your reply. Heming

[zhqingit]

Please remove the repeat SNVs in your SNV list file.

[hemingwang]

Hi Qing, In my snvs, a lot of points are the same position, but the annotation is different. For example, chr1 15664086 15664087 DDI2 0 + chr1 15664086 15664087 RSC1A1 0 + so how do I deal with this problem? I am looking forward to your reply. Heming

[zhqingit]

Hi Heming,

GIREMI identify the SNV based on only the chromosome, position and strand. So you can combine them to be one site.

Best, Qing

hemingwang notifications@github.com于2016年7月20日周三 下午11:19写道：

Hi Qing, In my snvs, a lot of points are the same position, but the annotation is different. For example, chr1 15664086 15664087 DDI2 0 + chr1 15664086 15664087 RSC1A1 0 + so how do I deal with this problem? I am looking forward to your reply. Heming

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[hemingwang]

Hi Qing, Thanks for your reply. I will revised snvs and try again by the way ,I cannot computed the ifRNAE, I dont't know how to deal with it. Heming

[hemingwang]

Hi Qing, When I revised snvs and try again,I met a new question. Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 1 Calls: cbind -> cbind -> data.frame I don't know how to deal with it. I am looking forward to your reply. Best! Heming

[zhqingit]

Hi Heming,

How many SNVs in your list? I guess the number is too small to generate the distribution of SNPs' MI.

Best, Qing

2016-07-21 5:54 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, When I revised snvs and try again,I met a new question. Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 1 Calls: cbind -> cbind -> data.frame I don't know how to deal with it. I am looking forward to your reply. Best! Heming

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[hemingwang]

Hi Qing, There are 10430 points in my SNVs list.

Best! Heming

[hemingwang]

Hi Qing, When I used a big snvs and try again,I met a new question: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 34 did not have 24 elements Calls: read.table -> scan Execution halted I don't know how to deal with it. I am looking forward to your reply. Best! Heming

[zhqingit]

Hi Heming,

Can you send me your SNV list and the intermediate file? I'd like to take a look.

Best, Qing

2016-07-25 8:28 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, When I used a big snvs and try again,I met a new question: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 34 did not have 24 elements Calls: read.table -> scan Execution halted I don't know how to deal with it. I am looking forward to your reply. Best! Heming

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[hemingwang]

Hi Qing, Here is my SNV list, out and out2.txt.Rout. Best! Heming snvs.txt out2.txt out2.txt .Rout.txt

[zhqingit]

Hi Heming,

I noticed there are lots of homozygous SNV in you list, which might affect your results. Please remove them.

Best, Qing

2016-07-25 16:13 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, Here is my SNV list, out and out2.txt.Rout. Best! Heming snvs.txt https://github.com/zhqingit/giremi/files/382670/snvs.txt out2.txt https://github.com/zhqingit/giremi/files/382671/out2.txt out2.txt .Rout.txt https://github.com/zhqingit/giremi/files/382673/out2.txt.Rout.txt

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[hemingwang]

Hi Qing, I don't the meaning of the "homozygous SNV", could I according to analyse the "vcf" document to remove the homozygous SNV sites? Best! Heming

[zhqingit]

Hi Heming,

In your SNV list, the reference or alternative nucleotide of some SNV is 0, they are the homozygous SNVs.

Best, Qing

2016-08-02 3:34 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, I don't the meaning of the "homozygous SNV", could I according to analyse the "vcf" document to remove the homozygous SNV sites? Best! Heming

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[hemingwang]

Hi Qing, Thank you for helping me. I will remove the homozygous SNV sites according your method and try again. At the same time , I use the GATK to get the snvs. When I use the GATK, there bam documents has been produced. There are {exp}_rg_added_sorted.bam, {exp}_dedupped.bam and {exp}_split.bam. Which bam document should I use in the GIREMI? The code is on the below: java -jar /mnt/tools/picard-tools-2.2.2/picard.jar AddOrReplaceReadGroups I={exp}.sam O={exp}_rg_added_sorted.bam SO=coordinate RGID={exp} RGLB=hg38 RGPL=HiSeq_2000 RGPU={exp} RGSM={exp} java -jar /mnt/tools/picard-tools-2.2.2/picard.jar MarkDuplicates I={exp}_rg_added_sorted.bam O={exp}_dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=output.metrics java -jar /mnt/tools/gatk/GenomeAnalysisTK.jar -T SplitNCigarReads -R /home/genomes/38.fa -I {exp}_dedupped.bam -o {exp}_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS I am looking for your reply! Best! Heming

[zhqingit]

Hi heming,

I am not familiar with GATK. I suggest you to read their manual to find detail information. The bam file you will feed to GIREMI should be the one used to call SNVs.

Best, Qing

2016-08-03 23:08 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, Thank you for helping me. I will remove the homozygous SNV sites according your method and try again. At the same time , I use the GATK to get the snvs. When I use the GATK, there bam documents has been produced. There are {exp}_rg_added_sorted.bam, {exp}_dedupped.bam and {exp}_split.bam. Which bam document should I use in the GIREMI? The code is on the below: java -jar /mnt/tools/picard-tools-2.2.2/picard.jar AddOrReplaceReadGroups I={exp}.sam O={exp}_rg_added_sorted.bam SO=coordinate RGID={exp} RGLB=hg38 RGPL=HiSeq_2000 RGPU={exp} RGSM={exp} java -jar /mnt/tools/picard-tools-2.2.2/picard.jar MarkDuplicates I={exp}_rg_added_sorted.bam O={exp}_dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=output.metrics java -jar /mnt/tools/gatk/GenomeAnalysisTK.jar -T SplitNCigarReads -R /home/genomes/38.fa -I {exp}_dedupped.bam -o {exp}_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS I am looking for your reply! Best! Heming

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[hemingwang]

Hi Qing, I will read the manual of the GATK. By the way ,could you please send the source code to me? I want to integrate the GIREMI to my system. My email is heming_wang@outlook.com Thank you! Best! Heming

[zhqingit]

Hi Heming,

May I ask you what system are you integrating? Thanks.

Best, Qing

2016-08-04 21:32 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, I will read the manual of the GATK. By the way ,could you please send the source code to me? I want to integrate the GIREMI to my system. My email is heming_wang@outlook.com Thank you! Best! Heming

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[hemingwang]

Hi Qing, We are working on an academic and non-commercial project regarding RNA editing, and we are willing to check and merge part of GIREMI in our RNA editing sites calling section to enhance the accuracy. As mentioned in a nature methods paper introducing GIREMI, the authors claimed that the source code would be released ASAP after its publication. If possible, could you please accept our application, and send me a source code copy without encryption. We will be very grateful for your support !
Cheers! Heming

[zhqingit]

Hi Heming,

Do you have personal email? We can talk more.

Best, Qing

2016-08-05 11:21 GMT-07:00 hemingwang notifications@github.com:

Hi Qing, We are working on an academic and non-commercial project regarding RNA editing, and we are willing to check and merge part of GIREMI in our RNA editing sites calling section to enhance the accuracy. As mentioned in a nature methods paper introducing GIREMI, the authors claimed that the source code would be released ASAP after its publication. If possible, could you please accept our application, and send me a source code copy without encryption. We will be very grateful for your support !

Cheers! Heming

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[hemingwang]

Hi Qing, I am very grateful for your reply! Here is my personal email heming_wang@outlook.com Cheers! Heming