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-   -   ENCODE ChIP-seq Metrics (NSC,RSC) (http://seqanswers.com/forums/showthread.php?t=27310)

apredeus 02-08-2013 06:35 PM

ENCODE ChIP-seq Metrics (NSC,RSC)
 
Hello all,

I was wondering if there's a software package that calculates the metrics that are used by ENCODE project (described in http://genome.cshlp.org/content/22/9/1813 )

I'm interested in NSC, RSC and data for "cross-correlation - strand shift" plots.

Anybody else uses those for their experiments?

Thank you in advance.

phansen 04-15-2013 07:34 AM

SPP package
 
Hi,

download and in install the spp R-package from here

http://compbio.med.harvard.edu/Supplements/ChIP-seq/

This package has a function 'get.binding.characteristics' which will do the job.

Peter

apredeus 04-15-2013 10:44 PM

Awesome, thank you for the advice!

mthornton 05-29-2013 03:11 PM

Hello,

I would use this script

https://code.google.com/p/phantompeakqualtools/

It uses SPP as well. It's convenient.

zgene 10-05-2016 01:42 AM

Quote:

Originally Posted by mthornton (Post 106014)
Hello,

I would use this script

https://code.google.com/p/phantompeakqualtools/

It uses SPP as well. It's convenient.

Dear All,

I am a newbie in ChIP-seq analysis and now I am trying to assess these values using "phantompeakqualtools", but unfortunately I got an error and cant find any similar posts for that.
Would you please help me !

I used this command to determine strand cross-correlation peak:

Rscript /data/NGS/phantompeakqualtools/run_spp.R -c=ChIP-WT1-R2-BWA_sorted_unique.bam -savp -out=R2unique-phantom

and I got the following error:

awk: line 2: function and never defined
Error converting BAM to tagalign file: /tmp/RtmpbkYntW/ChIP-WT1-R2-BWA_sorted_unique.bam6f036a95b6e

I assumed that the error was due to the input file and tried the following command to first convert BAM to tagalign

samtools view -F 0x0204 -o - ChIP-WT1-R1_sorted_unique.bam | awk 'BEGIN{OFS="\t"}{if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c > ChIP-WT1-R1_sorted_unique.tagAlign.gz

and again I got the following error;
awk: line 2: function and never define

So, now I know that the problem is due to awk. But I can't understand what it is exactly!

I would be happy to hear your comments.

Thanks in advance.


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