option to remove too short reads

[Zhuofei Xu]

Hi,

firstly many thanks for providing the nice tool for the sequencing data from microbial community!

I have a question if any option in kneaddata allows to remove all too short reads. I thought -a "SLIDINGWINDOW:4:15 MINLEN:75" can work but failed.

u0097639@GBW-P-SCI01:/mnt/nfs/data/zhuofei/test/metaphlan2/input/mouse$ kneaddata --input test.fq --threads 16 -a "SLIDINGWINDOW:4:15 MINLEN:75" -db /mnt/nfs/data/database/mouse/genome/ucsc/bowtie2/mm10 -o test
2015-09-24 11:28:33,223 INFO: Initial number of reads: test.fq: 25000
2015-09-24 11:28:33,224 INFO: Trimming...
2015-09-24 11:28:33,320 CRITICAL: Trimmomatic exited with exit status 1
2015-09-24 11:28:33,321 CRITICAL: Trimmomatic stderr:
TrimmomaticSE: Started with arguments: -threads 1 -phred33 test.fq /mnt/nfs/data/zhuofei/test/metaphlan2/input/mouse/test/test_kneaddata.trimmed.fastq SLIDINGWINDOW:4:15 MINLEN:75
Exception in thread "main" java.lang.NumberFormatException: For input string: "15 MINLEN"
        at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1250)
        at java.lang.Float.parseFloat(Float.java:452)
        at org.usadellab.trimmomatic.trim.SlidingWindowTrimmer.<init>(SlidingWindowTrimmer.java:15)
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:42)
        at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:282)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:40)


I also try the following option --trimlen 75
kneaddata --input test.fq --threads 16 --trimlen 75 -a "SLIDINGWINDOW:4:15" -db /mnt/nfs/data/database/mouse/genome/ucsc/bowtie2/mm10 -o test

The program run well and the output files are available. However, I can see some reads less than 75 nt are still there.

I'm wondering if it has an option to remove too short reads in the current version kneaddata v0.4.5.

Thanks in advance!

Zhuofei

[Andy Shi]

Hi Zhuofei,

Can you check the user manual? It's linked on the KneadData home page and is available here:

https://bitbucket.org/biobakery/kneaddata/src/4b831b7f42c35abc0bb8e393c799ee51ed1cf134/doc/UserManual.md?at=default&fileviewer=file-view-default

Check the "Specifying Additional Arguments" section. 

You need to do -a "SLIDINGWINDOW:4:20" -a "MINLEN:75" for this to work. 

The --trimlen argument is depreciated and doesn't work anymore. I will remove it in the next version. 

[Zhuofei Xu]

Thank you! It works

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