Hi all,
I am using prinseq to trim low quality tail of illumina reads. From the manual, I found -trim_qual_left and -trim_qual_right can trim seq by quality score from the 5' or 3' -end with certain threshold score. So, here are parameters I used:
I am not sure whether I chose correct parameter and whether 33 is too high.
In addition, I also used below two to trim polyA/T
When program was running, I checked the filtered out reads in so called 'bad_reads" file, I found the quality lines of most of reads contain a very long "#########", some of them even have entire line of #, e.g:
I am not quite clear the meaning of symbols in quality. Does multiple "#" really mean these sequences are bad? In "good reads" file, none of read contain "#" in its quality. I am afraid that I did anything wrongly and discard read which should be kept.
The version is illumina 1.9 based on fastQC.
Any advice is highly appreciated.
-alice
I am using prinseq to trim low quality tail of illumina reads. From the manual, I found -trim_qual_left and -trim_qual_right can trim seq by quality score from the 5' or 3' -end with certain threshold score. So, here are parameters I used:
Code:
#trim -trim_qual_right 33 -trim_qual_left 33
In addition, I also used below two to trim polyA/T
Code:
-trim_tail_right 10 -trim_tail_left 10
Code:
@HWI-ST538:217:C0NFWACXX:4:1101:19625:1943 1:Y:0:GAGTGG CNCGTCCCTTGATATGTTGTAATTCGTCTTTCATTTCCATTATGATGGCATCTGCAGCATCCTGCCAGAGACCTTTCAGATGAATATTTTCTTGCTGCAA + #################################################################################################### @HWI-ST538:217:C0NFWACXX:4:1101:20481:1941 1:Y:0:GAGTGG TNCATACTTTCGTTCCTTTCTCTTTATACGGATCGACTTCGTTCCAAGCTGTGGGAATCTTGACCGTGTTGTGCATCAGGGGTCATCTGCTTCGGTCATT + 3#02===@8<@?@7:=@?)>:>><>>@?9???8?4((--<(97<;):)7>7>???9?>???>)<>=99=?############################## @HWI-ST538:217:C0NFWACXX:4:1101:20349:1946 1:Y:0:GAGTGG CNGCGCTGCTGCCAACTAGTAAAGGAAGTATTCATTAAAATGCAGGGAGACCGCAGGAATGGGGACATGTTCCCCTTTGGGGACCCTTTTGGCAGCTTCG + ;#0@-55=?<>>>??9??>.8=9>@>@<?>?=?>?>????>?>?<<=5=???<??<?9>?########################################
The version is illumina 1.9 based on fastQC.
Any advice is highly appreciated.
-alice
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