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marcelm / cutadapt

Cutadapt removes adapter sequences from sequencing reads
https://cutadapt.readthedocs.io
MIT License
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Cutadapt produces emtpy FASTQ entries #231

Closed biocyberman closed 7 years ago

biocyberman commented 7 years ago

This is my original sequences:


@LD5V2:07687:11021
TTGTGTTTGAACGCTCTCTTAATTGGTGGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTT
+
6+3788808;6<<===;;;5<6;-3-371544/233,395:5==::<<<<3:99388079999)98464866..-4*-*-0000(0-22488975;;1666..,32
@LD5V2:07687:11026
TGATCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCAGAAGGTATAGGGGTTAGTCCTTGCTTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGACCA
+
6;9335977*6772999990959:;:<6<.53::19;39891845..*-36159<6;::::;;6;6>:95333)52577957*...*/6774999894726268858=>=-99:99:2;>3>5:::5:;;<;;::;7/,*,3***+,
@LD5V2:07687:11043
CATCTCATCCTGCGTGTCTCCGCTC
+
467976675/-----3444436566
@LD5V2:07688:11020
AAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCCCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACT
+
:::0:?4>7==<<4<;;;=<=7;78888.9;@><5;;4:4:4:4:;;2;<<<6<<6<<=4>6;;<=2;;;;;5565533'5::/;<2<?ABD?7<<<;5<=
@LD5V2:07688:11051

When I ran cutadapt version 1.12 like this:

cutadapt -b CCATCTCATCCCTGCGTGTCTCCGACTCAG -b CCTCTCTATGGGCAGTCGGTGAT -o out.fastq --trim-n -f fastq in.fastq

The entry @LD5V2:07687:11043 got written out to out.fastq with empty content:


@LD5V2:07687:11043

+

This picardtools does not allow.

marcelm commented 7 years ago

Hi, sorry for very brief reply, not working now. picardtools is wrong IMO, but to fix it, use cutadapt with -m 1 to filter empty reads.

biocyberman commented 7 years ago

I overlooked the -m option. And I agree with you that picard is overreacting in this case :) Thank you.