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Raw sorted cashmere from gathering centres is sent in bales by trucks or by train to Bandar Abbas and Khoramshahr, the main Iranian exporting ports in the Persian Gulf.
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Here C i,s is the size of chromosome i ; N i,c is the number of raw flow-sorted chromosome sequence reads aligning to chromosome i ; N i is the number of mapped reads from flow sorted chromosome sequence library i.
Before any material can be recycled, it must be separated from the raw waste and sorted.
For the TMM13 method, the results are shown for the sorted RAW confidence scores as presented in [12].
We developed a customized pipeline that takes individually sorted raw sequences and outputs files ready for SNP calling.
SLAF marker identification and genotyping were performed using procedures described by Sun et al. Briefly, low-quality reads (quality score <20e) were filtered out and then raw reads were sorted to each progeny according to duplex barcode sequences.
The raw sequences were sorted based on unique barcodes, trimmed for sequence quality, and clustered at 97 % identity for OTUs with USEARCH v7.0 (http://www.drive5.com/usearch/download.html) using UPARSE pipeline [ 46].
The raw reads were sorted according to indices, and the high-quality SNPs between parents were called by alignment with B73 RefGen_v2 sequence (http://www.maizegdb.org) using BWA package [ 20, 55] and Genome Analysis Toolkit (GATK) [ 56].
By using standard PHP functions, the adjustment is performed from a sorted list of raw P-values and the number of data sets (24).
All reads for total RNA-seq and small RNA-seq were sorted based on quality, and raw sequences with removed 3' linker sequences were obtained in FASTQ format.
The adaptor-sorted and PCR duplicate-free raw sequencing data is available at GEO (Accession number: GSE61730) along with the three expression matrices that contain the median-normalized values for the respective samples after full processing of the raw data.
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