Dear all,
revealing batch effects in sequencing data may be a difficult task.
We have designed a new R-package (seqTools) which may be able to detect batch effects in compressed Fastq files (and does some other standard QC tasks). The package is currently available on R-forge:
from where the source and a windows binary can be installed using the standard mechanism:
install.packages("seqTools", repos="http://R-Forge.R-project.org")
We analysed 61 RNA-seq samples and found a remarkable prevalence of batch effects. A preprint of the results is available from
It would be great to get feedback or suggestions from anyone who might find this useful.
Thanks
revealing batch effects in sequencing data may be a difficult task.
We have designed a new R-package (seqTools) which may be able to detect batch effects in compressed Fastq files (and does some other standard QC tasks). The package is currently available on R-forge:
from where the source and a windows binary can be installed using the standard mechanism:
install.packages("seqTools", repos="http://R-Forge.R-project.org")
We analysed 61 RNA-seq samples and found a remarkable prevalence of batch effects. A preprint of the results is available from
It would be great to get feedback or suggestions from anyone who might find this useful.
Thanks
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