Question on QuEST

[kopo3]

Hello, all.

I am trying to process our ChIPseq data using QuEST.

http://mendel.stanford.edu/sidowlab/downloads/quest/

I have managed to compile the program and succeeded in processing the sample data on the homepage above.
However, when I tried to do the same thing with our data, QuEST displays errors and I cannot process the data.

Below is several lines of our data,
GGTGCCCTGCTTCCTTGCCATTCCAGCCATGCCTGA 0 0 chr6:136088939 F
GTTTAGCAGTGGTTCCAGAGGACTTAATAGACAGAA 0 0 chr6:43415552 F
TAAACTCTTACAACCTAAAGCTCTAAGTCCTTAGGA 0 0 chr13:86619993 F

and this is the error that I keep getting.
. Skipping.pected +/- for orientation of read but found F
. Skipping.pected +/- for orientation of read but found F
. Skipping.pected +/- for orientation of read but found F

What is wrong with our data? I hope some of you can help us out.
Thanks in advance.

[Xi Wang]

Hello, all.

I am trying to process our ChIPseq data using QuEST.

http://mendel.stanford.edu/sidowlab/downloads/quest/

I have managed to compile the program and succeeded in processing the sample data on the homepage above.
However, when I tried to do the same thing with our data, QuEST displays errors and I cannot process the data.

Below is several lines of our data,
GGTGCCCTGCTTCCTTGCCATTCCAGCCATGCCTGA 0 0 chr6:136088939 F
GTTTAGCAGTGGTTCCAGAGGACTTAATAGACAGAA 0 0 chr6:43415552 F
TAAACTCTTACAACCTAAAGCTCTAAGTCCTTAGGA 0 0 chr13:86619993 F

and this is the error that I keep getting.
. Skipping.pected +/- for orientation of read but found F
. Skipping.pected +/- for orientation of read but found F
. Skipping.pected +/- for orientation of read but found F

What is wrong with our data? I hope some of you can help us out.
Thanks in advance.

I am wondering if you used the option -solexa_align_ChIP followed by your input file.

[kopo3]

Thanks for the reply.

I am wondering if you used the option -solexa_align_ChIP followed by your input file.

Dear Wang.

Thank you for your quick reply.
Actually, the command line I used was,

./generate_QuEST_parameters.pl -solexa_align_ChIP ./data_file.txt -gt ./genome_table -ap ./QuEST_analysis -ChIP_name DBF_CELL

Curiously, when I carried the command out in a cygwin environment, I did not encounter this error, although in the latter part of the process, the program ceased to work due to another error.
However, when I carried it out on a 64bit Fedora9 environment (in which I was successful in processing the sample file on the original homepage) I got this error.
Do you have any idea what is wrong with the data, or command line?

[Xi Wang]

Dear Wang.

Thank you for your quick reply.
Actually, the command line I used was,

./generate_QuEST_parameters.pl -solexa_align_ChIP ./data_file.txt -gt ./genome_table -ap ./QuEST_analysis -ChIP_name DBF_CELL

Curiously, when I carried the command out in a cygwin environment, I did not encounter this error, although in the latter part of the process, the program ceased to work due to another error.
However, when I carried it out on a 64bit Fedora9 environment (in which I was successful in processing the sample file on the original homepage) I got this error.
Do you have any idea what is wrong with the data, or command line?

That is quite abnormal. Waiting for the author to answer...

Days ago, I also encountered an error when running QuEST 2.4. I think it would be a common problem. So I post it here.

I found that in the file "run_QuEST_with_param_file.pl": Line 742

my $pseudo_ChIP_scores_path = $scores_path . "/pseuod_ChIP";

there is a misspelling: "/pseudo_ChIP" instead of "/pseuod_ChIP".

This misspelling will cause the program stoped with an error message:
>> bad file name: ./scores/pseudo_ChIP/chr1.score
>> run_generate_profile_with_param_file.pl: Caught an error message (code 256), passing error message to the top script.
>> run_QuEST_with_param_file.pl: Caught an error message (code 768) when running generate_pseudo_ChIP_profile. Aborting.

[kopo3]

The original file that I had was an eland-extended file.
I converted the file so that it was similar to the example file.
I noticed that I could use an option so that QuEST can analyze eland-extended files and it worked!
So, although I still do not know why QuEST could not handle the file I converted, it seems that I can use QuEST to analyze files that we have.

Thank you!

[Anton]

Hi kopo3, my guess is that the solexa align file is messed up in some way, e.g. has tab as a separator instead of a space.

Xi, thanks for catching the pseudo_ChIP typo - I had fixed this bug and posted a new version on my web site:

http://www.stanford.edu/~valouev/QuEST/QuEST.html

Here's the direct link:

http://www.stanford.edu/~valouev/QuEST/QuEST_2.4.tar.gz

Very best! Anton.

[ikrier]

Problem using quest with illumina 1.3+ files

Hi,
What is the option for using eland_extended files as input? I have alignment files of the latest format (1.5.1 pipeline version). They look like this :
R2D2 1 5 12 894 524 1 AGAGAGCAGGCTGAGACTACTAGGTGTGGGCAT eegggefgggfegeggggf`gTLTLITNPRSff chr10 3002722 F 3C29 55
R2D2 1 5 31 1197 1453 1 AGAGAGCAGGCTGAGACTACTAGGTGTGGGCAT ggggggdgghegcggghggfggegcgfdgc chr10 3002722 F 3C29 57

It doesn't seem to be recognized in default mode. From the manual I have, something different is expected. I can reformat the files to extract the info, but if there's an option already there, it'd be so much easier.

[Anton]

Folks, please post your questions regarding QuEST into the QuEST Google group:

http://groups.google.com/group/chipseq?lnk=iggc

It is much easier for me to handle questions there.
Much appreciated!
Best, Anton.

[Bioinfo]

Hi all,
Do anyone has experience with Quest for chipseq data analysis. anyone can suggest how to use eland alignment files(export/sorted). however i tried and met some errors as posted above.
thanks in advance