SOAP

[…] generated per long rna library and small rna library, respectively. the clean reads produced from the long rna libraries were first mapped to the homo sapiens rrna database using the soapaligner/soap2 short read alignment software, to remove the remaining rrna reads. the non-rrna reads were used to perform the transcriptome assembling and quantification. first, non-rrna reads were mapped […]

[…] a standard illumina shotgun library was constructed and sequenced using the illumina hiseq 2000 platform; this generated 8,355,450 clean reads totaling 752 mbp. these reads were assembled using the short oligonucleotide analysis package (soapdenovo v2.04) with all parameters set to default [21]. the final draft assembly contains 25 contigs in 8 scaffolds. final assembly was based on all clean […]

[…] genome sequence and gene profiles of p. aeruginosa pao1 (genbank accession number: ae004091). the software tophat37 was used to map mrna sequences to the genome, and subsequently the combination of soap2 program38 and cufflinks39 was used to calculate the expected fragments per kilobase of transcript per million fragments (fpkm) sequenced. finally, the differentially expressed transcripts […]

[…] for the bioinformatics analyses., in consideration of rrna pollution interference in the analysis, the clean reads were mapped to an rrna reference sequence using the short reads alignment software soap2 (http://soap.genomics.org.cn/) to remove the remaining rrna reads. the remaining reads were used for transcriptome assembly and quantification., the removed rrna reads were mapped […]

[…] to the arabidopsis col-0 (tair10.0) nuclear-encoded cds gene set, the mitochondria-encoded cds gene set and the chloroplast-encoded cds gene set, respectively. the alignment tool is soapaligner/soap2 (parameters: -m 0 -× 10,000 -s 40 -l 32 -v 5 -r 2 -p 6) [41]. the transcript abundance was estimated by the rpkm (reads per kilobase transcript per million reads) calculation for each gene […]