Removing poly-A tail

[Behnaz64]

Hello

I have done paired-end sequencing and need to remove poly-A and poly-T sequences from R1 and R2 reads. Based on the manual, I ran this command:

fastp -x -i AH1_R1.fastq -I AH1_R2.fastq -o AH1-R1-trimmed.fastq -O AH1-R2-trimmed.fastq

I also tried --trim_poly_x option, but it seems that the sequences are not removed, as the base content plot after filtering for read1 still shows an excess of A (44%). Could you please tell me what I should do to fix the problem?

Thank you

[Behnaz64]

I also tried preparing a FASTA file containing the poly-A and poly-T sequences and submitting it through the "--adapter_fasta" option, but no success.

[sunta3iouxos]

for some reason I am on the same boat. used --trim_poly_x and --trim_poly_g options

./fastp -i A006850047_113702_S1_L002_R1_001.fastq.gz -o A006850047_113702_S1_L002_R1_001_trim.fastq.gz -I A006850047_113702_S1_L002_R2_001.fastq.gz -O A006850047_113702_S1_L002_R2_001_trim.fastq.gz --unpaired1 A006850047_113702_S1_L002_R1_001_unpaired.fastq.gz --unpaired2 A006850047_113702_S1_L002_R2_001_unpaied.fastq.gz --failed_out A006850047_113702_S1_L002_R2_001_failed.fastq.gz -Q --correction --trim_front1 16 --overrepresentation_analysis --detect_adapter_for_pe --trim_poly_x --trim_poly_g --split 10 --json /projects/ccg-ngs/fastq/LR05/A006850047_113702.json --html /projects/ccg-ngs/fastq/LR05/A006850047_113702.html --report_title /projects/ccg-ngs/fastq/LR05/A006850047_113702

fastp 0.20.1, at 2020-06-08 17:11:37

[saramoussadeq]

i have the same problem too. --trim_poly_x and --trim_poly_g didn't remove all the poly-X I can't undertand why.