SNP Map file help...JMP Genomics importing Illumina SNP data across multiple files<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />Total newbie to JMP Genomics 6.0. I have the SNP final report data generated by Illumina studio software. The dataset contains 512 total samples, each with around 1E6 markers. The Final Report.txt files were split up over 13 txt files. I also have the Samples Table.csv that I converted to a tab-delimited file, so I assume I have the "sample files" selection satisfied.
The data import for Illumina supports spanning multiple genotype files, however it clearly indicates a SNP Map File is necessary when multiple genotype files are selected. My guess is to help assemble the multiple files together?
I cannot find an example of what the SNP Map File (or to double check, what the Sample Files is supposed to contain). I tried to see if there was a sample data set to help, but did find one.
Any help is greatly appreciated!
Thanks!
Jonathan
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesWe've taken a look at all of this, and there seems to be some issue with the sample and the map files. Here's how you can work around all that. First, import the final report, and set the Length of Sample ID column to 32 in the options tab. I used Top and the rs values for the import, but you can select all if you want all the markers - just be sure to keep the common prefix - you'll need it.. Run the import. This will generate a map file with the column IDs (which will have underscores) and the initial ID (which will have dashes).
Open the txt map file and File>Save As SAS data set. Merge (or Tables > Join in JMP) with the map file created by the import using the original column names as the matching variable. Save the result as a SAS data set if you did the join in JMP and not the Genomics data set utilities merge function.
Open the samples txt file and save as a sas data set. Use the Data Set Utilities Merge function to merge this with the imported marker file. The Sample data set should be the first entry into the dialog window as you want that to the left of the merged data.
Then run the Subset/Reorder from the Genetics Utilities. to get the data set and map file ordered. Note that you will be specifying the markers with the common prefix as a List-Style specification. Eg, SNP_: (there's a colon there).
Contact me directly if you get stuck.
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesHere's a link to one of the final report files:
https://www.dropbox.com/s/wguj9t6wdnra0re/EA07060_2013-01-25_FinalReport1.txt
I don't think there is anything wrong with the final report files, though...I can create an JMP genomics project from any of the individual files (and I don't have to include either a sample table or SNP map file). So I was assuming it was one of these two files as the problem when trying to create a project with all 13 final reports.
Let me know if this final report file helps!
Thank you dougR!!
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesThe map file looks fine so far as I can tell.
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesOkay, I can send you one of the final report files (via dropbox)
The final report files do have all the genotype calls:
| SNP Name | Sample ID | Allele1 - Top | Allele2 - Top | GC Score | Sample Name | Allele1 - Forward | Allele2 - Forward | X | Y | X Raw | Y Raw |
| exm-rs10067427 | 1969-01A_02-008-1 | A | A | 0.9536 | 1969-01A_02-008-1 | A | A | 1.2 | 0.03 | 8235 | 199 |
| exm-rs10068788 | 1969-01A_02-008-1 | A | A | 0.9073 | 1969-01A_02-008-1 | A | A | 0.352 | 0.015 | 2445 | 99 |
| exm-rs1006899 | 1969-01A_02-008-1 | A | A | 0.9335 | 1969-01A_02-008-1 | A | A | 1.049 | 0.03 | 7204 | 193 |
| exm-rs10069397 | 1969-01A_02-008-1 | A | A | 0.897 | 1969-01A_02-008-1 | T | T | 0.514 | 0.049 | 3676 | 295 |
| exm-rs10071490 | 1969-01A_02-008-1 | A | A | 0.914 | 1969-01A_02-008-1 | A | A | 0.677 | 0.065 | 4664 | 321 |
| exm-rs1007358 | 1969-01A_02-008-1 | A | G | 0.9287 | 1969-01A_02-008-1 | T | C | 0.675 | 0.617 | 4678 | 2626 |
However, JMP asks that for a dataset that spans multiple final reports (I have 13 total) I need to include a Sample Table...I'm presuming to help assign which final report file contains which samples since the FinalReport files have the genotypes, not the Sample File.
Does the SNP_Map file look okay?
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesYou definitely need the Genotypes. They are often AA, AB, BB format. Also, I noticed that there is just one line per individual. This file should contain all the calls with the SNP ID and the individual ID.
The final report is another option and may have the needed format. If you want to send one to me by dropbox or some other method, send an email directly to me with the info and I'll check it out.
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesThanks doug! What values are supposed to appear in that column?
I can ask the core to re-export the Samples Table, but are there other empty columns on there as well, so do they all need values?
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesIt looks as if the Genotype column does not contain any values in the Samples Table. That could be the problem.
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesSure thing!
I can arrange to send a final report if necessary, 13 final reports at 3.2 gb per report.
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesHi Jonathan - is there any way you could share some of these files so we could take a look?
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesHi Doug,
I updated the map file to only contain three columns: SNP_Name, Chr, and Position. The first row contains those headers, the remaining 953891 rows have all the SNP map data. This is a text delimited file as are my 13 final report files and my sample table file.
Trying to import the data, I still get the same error:
Starting skip_header_import_2
DataFile = E:\Genotype final report\SNP_Mapv2.txt
DataType = TAB
VarNameRow = 1
VarLabelRow = 0
UniqueVarNameFlag = 1
NOTE: UNBUFFERED is the default with RECFM=N.
NOTE: The infile "E:\Genotype final report\SNP_Mapv2.txt" is:
Filename=E:\Genotype final report\SNP_Mapv2.txt,
RECFM=N,LRECL=32767,File Size (bytes)=23782301,
Last Modified=18Oct2013:15:47:43,
Create Time=18Oct2013:15:47:43
NOTE: Unexpected end of file for binary input.
NOTE: DATA statement used (Total process time):
real time 1.62 seconds
cpu time 0.01 seconds
22: LINE and COLUMN cannot be determined.
17 The SAS System 15:50 Friday, October 18, 2013
NOTE 242-205: NOSPOOL is on. Rerunning with OPTION SPOOL might allow recovery of the LINE and COLUMN where the error has occurred.
ERROR 22-322: Syntax error, expecting one of the following: a name, a quoted string, a numeric constant, a datetime constant,
a missing value, INPUT, PUT.
NOTE: The SAS System stopped processing this step because of errors.
NOTE: DATA statement used (Total process time):
real time 0.03 seconds
cpu time 0.00 seconds
skipbyte to scan column name line: 0
NOTE: UNBUFFERED is the default with RECFM=N.
NOTE: The infile "E:\Genotype final report\SNP_Mapv2.txt" is:
Filename=E:\Genotype final report\SNP_Mapv2.txt,
RECFM=N,LRECL=256,File Size (bytes)=23782301,
Last Modified=18Oct2013:15:47:43,
Create Time=18Oct2013:15:47:43
flag=1 VarName=SNP_name columnpt=10
flag=2 VarName=Chr columnpt=14
flag=3 VarName=Position columnpt=23
flag=4 VarName=200610-179 columnpt=34
flag=5 VarName=chrY columnpt=39
flag=6 VarName=18097249 columnpt=48
flag=7 VarName=200610-298 columnpt=59
flag=8 VarName=chrY columnpt=64
flag=9 VarName=14926202 columnpt=73
flag=10 VarName=200610-303 columnpt=84
flag=11 VarName=chrY columnpt=89
flag=12 VarName=23497067 columnpt=98
Ugggh, not sure what I'm missing. Any ideas?
If I just use the import engine for a single final report (which does not require a SNP map file) it works fine, but I need to load all 13 final reports...so this makes me still think I have something wrong with the SNP map file.
Thanks!
Jonathan
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesHi Johnathan
You name the variables, SNP_Name, Chr and Position. You only need one position column. Please also make sure that the delimiter is the same as the genotype file.
Doug
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesWanted to provide an update...getting closer, I think.
I now have a SNP-Map.txt file, but I think there is something missing in the file as I get the following error:
ERROR 22-322: Syntax error, expecting one of the following: a name, a quoted string, a numeric constant, a datetime constant,
a missing value, INPUT, PUT.
In the SNP_Map.txt file from the core it does not look like there are column headers, simply:
line1: track name="HumanOmniExpressExome-8v1_B"
line2: chr14 35173623 35173624 exm-rs10139660
and all the other SNPs on the chip.
Should I reorder and put in a header line with something? SNP, Chr...what would I title the two position headers?
I think I am close
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesHi Doug,
Sounds great. I've asked for the file that contains that info and will give it a shot! Also, I'm checking out those guides...should be a great help. Will report back ASAP.
Best,
Jonathan
Re: SNP Map file help...JMP Genomics importing Illumina SNP data across multiple filesHi Johnathan.
The SNP map file is a txt file that contains the SNP Name, Chr and Position variables. You should be able to get the complete map file for your chip from the core lab.
You can find a number of step-by-step guides for JMP Genomics here:
http://www.jmp.com/lifesciences-resources/resources.shtml?tab=1
Doug Robinson
JMP Life Sciences Specialist
