Amazon air fungi

Description

Fungal large subunit ribosomal rDNA amplicons and shotgun metatransctipome sequence data and metadata for fungal communities in the atmosphere above the Amazon rainforest canopy in Brazil. Data collection procedures are described in the paper "Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest" by Womack et al. (manuscript submitted to Biogeosciences).

LSU files:

amazon_air_fungi_metadata.txt - A tab-delimited text file with information on barcode and primer sequences and date of sample collection. The columns of the text file include a sample identifier (SampleID), barcode sequences (BarcodeSequence), reverse primer sequence (LinkerPrimerSequence), and the date of sample collection (Description).

R3bc_R1_052913_062813ax.fastq - Raw LSU sequence data in FASTQ format, produced by a sequencing run using Illumina MiSeq 150bp paired-end sequencing technology. Due to file size limitations, the original tar/gzip archives have been split into multiple parts.

Metantranscriptome files:

metatrans_barcode_file_edit.txt – Barcode file used for demultiplexing with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).

Raw metatranscriptome sequences produced by a sequencing run using Illumina HiSeq 150 bp paired-end sequencing technology. The paired-end sequences were joined using fastq-join (https://code.google.com/p/ea-utils/wiki/FastqJoin) and then demultiplexed using FASTX with the commands below:

#join raw forward and reverse reads using fastq-join

./fastq-join raw_R1_cat.fastq raw_R2_cat.fastq -o raw_cat_

#barcode split

cat raw_cat_un1.fastq | fastx_barcode_splitter.pl --bcfile metatrans_barcode_file_edit.txt --bol --prefix R1_unjoined

cat raw_cat_un2.fastq | fastx_barcode_splitter.pl --bcfile metatrans_barcode_file_edit.txt --bol --prefix R2_unjoined

cat raw_cat_join.fastq | fastx_barcode_splitter.pl --bcfile metatrans_barcode_file_edit.txt --bol --prefix joined

For each sample day (Dec. 8, Dec. 9, Dec. 11) there are three files, R1_unjoined, R2_unjoined, and joined. The three files may have been split into multiple parts (ax).