标签:
In this example we have 5 pair of fastq files in three different subdirectories. The file to process can be specified with "*/*.qf.fastq" and veriied with ls.
$ ls */*.qf.fastq run1/s_1_1_sequence.qf.fastq run2/s_2_2_sequence.qf.fastq run1/s_1_2_sequence.qf.fastq run3/s_1_1_sequence.qf.fastq run2/s_1_1_sequence.qf.fastq run3/s_1_2_sequence.qf.fastq run2/s_1_2_sequence.qf.fastq run3/s_2_1_sequence.qf.fastq run2/s_2_1_sequence.qf.fastq run3/s_2_2_sequence.qf.fastq
Next, we issue the jellyfish count command
jellyfish count -t 8 -C -m 25 -s 5G -o spec1_25mer --min-quality=20 --quality-start=33 */*.qf.fastq
First confirm that you got the output file
$ ls spec1_25mer* spec1_25mer_0
now that there is a single file spec1_25mer_0
$ jellyfish histo -o spec1_25mer.histo spec1_25mer_0
Confirm that you got the output
$ ls spec1_25mer* spec1_25mer_0 spec1_25mer.histo
Examine the numbers by your eyes
$ head -25 spec1_25mer.histo 1 461938583 2 95606044 3 19280477 4 13836754 5 11018480 6 9555090 7 8557935 8 7863244 9 7319505 10 6920880 11 6589723 12 6321923 13 6148638 14 6036120 15 5972264 16 5962234 17 5987696 18 6051171 19 6154429 20 6297373 21 6485135 22 6700579 23 6932570 24 7217627 25 7533211
jellyfish K-mer analysis and genome size estimate
标签:
原文地址:http://www.cnblogs.com/freemao/p/4847168.html