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View Process HV 01

Concatenate Files

cat HvCatNor7_L1_1.fq HvCatNor7_L1_2.fq > HvCatNor7_L1.fq

Assembly with Trinity

/opt/trinity/trinityrnaseq_r2011-07-13/Trinity.pl —seqType fq —single HvCatNor7_L1.fq —CPU 4 —run_butterfly —bflyHeapSpace 10G

Results

grep -c ‘>’ trinity_out_dirHvCatNor7_L1.fq/Trinity.fasta
63131
Total length of sequence: 52315803 bp
Total number of sequences: 63131
N25 stats: 25% of total sequence length is contained in the 4565 sequences >= 2123 bp
N50 stats: 50% of total sequence length is contained in the 12527 sequences >= 1302 bp
N75 stats: 75% of total sequence length is contained in the 26487 sequences >= 660 bp
Total GC count: 20930030 bp
GC %: 40.01 %
grep ‘>’ Trinity.fasta | sed ‘s/len=//’ | awk ‘{print $2}’ | sort -n
LargestContig:5349
ShortContig:200