Quality check for genomic reseq data and aligment to reference genome

Question

[kirannbishwa01]

I was able to do preliminary data quality analysis on RNAseq data (fastq format) using both fastqc and prinseq. But, the same app isnot able to do quality analysis for resequence genomic data (which is also in fastq format).

Is there some other app for doing quality checks for genomic reseq data.

Additional question:

The genomic reseq data is for different population of A. lyrata. I have reseq data from two different populations (6 individuals per population). What apps combination provide best approach to get this data aligned to reference sequence?

Thank you!!!

[Prakki Rama]

fastqc should work on genomic data as well. Do you see any error?

[kirannbishwa01]

I got the following message in log file for both fastqc and prinseq:

log4j:WARN No appenders could be found for logger (clojure-commons.config).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

This message was in the file named 'condor-0-input-0-stderr'. However the app works well with RNAseq data.