adapters not removed - mismatches insertion/deletion

[marilyne9]

Hello,

I used this option --detect_adapter_for_pe to remove adapters but some adapters were still there in my contigs after assembly. I noticed mismatches that are insertion/deletion in the adapters I am wondering if fastp can recognize mismatches that are insertion/deletion and detect adapters with one deletion?

Here is my command line: ./fastp --in1 JC-0001_S929_L001_R1_001.fastq.gz --in2 JC-0001_S929_L001_R2_001.fastq.gz --out1 JC-0001_S929_L001_R1_001.cleaned.fastq.gz --out2 JC-0001_S929_L001_R2_001.clened.fastq.gz --correction --cut_front --cut_tail --detect_adapter_for_pe

Best regards,

Marilyne

[sfchen]

Could you please paste some reads here, whose adapters couldn't be removed.

[marilyne9]

Hello,

I can give you one alignment with a contig and one adapter for example: in the contig or initial read there is a 'C' inserted

NODE_89_lengt 9213 GGCCTCGTCCT 9223 ||||| ||||| adapter2 1 GGCCT-GTCCT 10

[sfchen]

Please give me the reads containing this adapter.

I will debug it with fastp.

[marilyne9]

I do not know which read it was originally. There are millions of reads. This adapter was in only in one contig at the end. Maybe I could map the reads to the contig but it is not so easy to identify which read was not trimmed. Do have some ideas why?

[marilyne9]

Hello, Here are few reads:

@A00814:76:HNLLGDSXX:1:1101:29369:1000 1:N:0:NTGGTTGACT+GGCCTGTCCT TCCTCCTCCTCCTCCTCCGAATCTCCACTCAAAAAGACAAAGTCCTCCTCCGAGTCCTCCTCCGAGTCCGAACTCGACTCCGAGACGGACGAAACCGCCCGCGAGTCTGCGCCGACCGACCGCACGGCCGACTCAAACTCGCTCAGGTT + FFFFFFFFFFFFFFFFFFF,:,FFFFFF,F:FFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFF @A00814:76:HNLLGDSXX:1:1101:29912:1000 1:N:0:NTGGTTGACT+GGCCTGTCCT GTGCGTACTGACTCTGATCAGAATTGATTACCTGCCATGTGCGTGGGGGAAACTGACAACGGGGCATCTCCTTTCTCCAGAGCGGCGGCGGCAACGACGACGAGGCGCCTGATTCCCTCCTCGAAATGGCCGCCGAGATGGAACGCACCG + F:FFF,FFFFFF,FFF:FF,F::FFFFFFFFFFFF,FFF:FFFFFF:FFF:,FFFFF:FFFFFFF::FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFF,F,FFFFFFFFFFFFFFFF,FFFFFFF @A00814:76:HNLLGDSXX:1:1101:31539:1000 1:N:0:NTGGTTGACT+GGCCTGTCCT CGCAAGACGACTCACGGGCGAATCGCTATCCGCACGACGGTGTGGTAAAGGTCTGCCAACTCGCCCCGCTTGACCGAGACGGCCAACGGGACTCGGATCGACAACTTGCGGCAGTACGTATCCGGCTGGACTTCGTGGCGCTGTTTCGCG + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00814:76:HNLLGDSXX:1:1101:1841:1016 1:N:0:NTGGTTGACT+GGCCTGTCCT CCTTATAGTGTTTATGTAAGTATAAGATAGGTATGTATGGCATGTGATGTAATTATACGTATCTTATATGACACTTCCTACTAATAGTAACGTCGAGTCTTCTTGACCATCGTATAGACTATCATTGCTATACGTTTCTATCGTGAAGGG + FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF,FFFFF:F

[marilyne9]

Hello, Is it what you need ?

[marilyne9]

Hello, may I have some help to debug ?

[sfchen]

Hi, I will debug within some days.

[wfgui]

Hi, I will debug within some days.

I had the same problem， can't remove read2 adapters

[y9c]

Hi @sfchen,

I have also found that fastp can not deal with "read through" reads correctly.

A diagram from Trimmomatic:

Read1 fastq file:

@K00159:45:H4W76BBXX:5:1105:20791:9167 1:N:0:CAACTA
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCATCTGCCAGAAAAAAG
+
AAFFFJJ7JFFFJJJFAFJJJJJJJJFJJJFJJAFJJAJA-F7JJFFAJFJJJJJJJJJJ<-FJJJJJJJ<JFJFAF-<JFJFJJAJJJFJFJJJFJJFFJ<FAF<FFJFJJ7JJJJJJJJJ-FF-FJAJFJ
@K00159:45:H4W76BBXX:5:1105:12063:9027 1:N:0:CAACTA
CCGACTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAATTTTTTTAAAAATTTACCTCCACAACCGCAAGCACAACGTACAAAGAATTCCGGGCGCACGGGCCCGACCG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

Read2 fastq file:

@K00159:45:H4W76BBXX:5:1105:20791:9167 2:N:0:CAACTA
CGTCGTCCGGCTGTACACCTCTCAAGGTGTACTTCTCGGTGGCCGTATCATTATTAAAAACTTTTTTTCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+
A--77FFJ-<FF-FFF-AF7AJA-JJJ-FFF-<<J-F-FA-<F-AA-<<-<AAA-FF---AAFFAAJAF-7-<F-7AJFA<FJAAAJFAJJF<A-<7AJFF7-FF-<-<-<7FF<7FFFJAF-7<AFAA<J<
@K00159:45:H4W76BBXX:5:1105:12063:9027 2:N:0:CAACTA
CAGTCGGGATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAATTTTTTTCAAGCAGAAGACGGCACACCAGATTAGTTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACTCAG
+
AAFFFFJFFJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJFJFJJJJJJJJJJJJJFJJJJJJJJJJJJJAJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFFFJFFJJJ

[y9c]

fastq can not deal with some adapters in SE mode either. for example:

@K00159:45:H4W76BBXX:5:1103:11931:62171 1:N:0:CAACTA
GAGGACGAGGAGATCGGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAACAAAACACGCCTATCGCCGGCGAAGTCCGGAAACAAGCAAAACAAAAGTCCAACCGGGGGAGAGCCTAC
+
AAAFFFJ7JJJAFFFA-AJJJJJJJJJJJJJJJJJJJJJJJAJFJJJJJJJJJJJJJJJJJJJJJJJJFFJFJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJ-FAJJJFJA7FJJJJJJJJJJJJJJJJJJFFJJFJJFJFJF
@K00159:45:H4W76BBXX:5:1103:19157:62277 1:N:0:CAACTA
GAAAGTCGGAGATCGGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAGAACGGTGGTGCCCCGCTGGGAGAGGTTAACCACAACAAGAAAAATAAATGTCGCCACTGAGGCCAAC
+
AAFFFFJFJJJJJAFFJFJJJJJJJJAJJAJFJA<FFJFFJ<JJJJJJJJAFFJFJJJJJJJJJJJJFFFFJFFJJJJJJJJJJJJJJFFJJFJF<JJJJJJJJFJFAFAJJJFFJFFJFFJAAJJJAJJAJJJJJAFFFJJJJFJJJJJ
@K00159:45:H4W76BBXX:5:1103:15270:63032 1:N:0:CAACTA
AGATCGGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAATTTTTTTTTAATGTTCGGCGACCCCCCGGGATTTACCCTTCCAAAGTTTAAAAGCCCGCCGACCGGGCGGGGAAGGGA
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJF

(Illumina Trueseq read1 adapter)

[EisenRa]

Just thought I'd update this, as it would be nice if sequencing errors in the adapter sequences could be taken care of.

Adapter used for R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

All of these get successfully trimmed, but it seems that sequencing errors/insertions/deletions in the adapter sequence are not taken care of:

(The second sequence in each e.g. is the adapter sequence without error)

e.g. 1 AGAGATCGGAAG**_**GCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

e.g. 2 AGATCGGAAGAGCACACGTCTGA**_**CTCCAGTCA AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

e.g. 3 AGAGATCG**_**AAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCACACGTCTGAACTCCAGTCA