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Old 11-19-2019, 10:31 PM   #1
Kujin Kwon
Junior Member
 
Location: Korea, South

Join Date: Dec 2018
Posts: 9
Default Odd sequences in RNAseq fastq

Hi all,

Recently, I just ran iSeq for pair ended RNA sequencing and it gave me odd fastq results
Some of Read1(i7) sequences have Adapter sequences with poly G at the end.

@FS10000436:35:BPC29621-1807:1:1101:10010:1370 1:N:0:1
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGCGAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

However paired Read2(i5) sequences gave me random and poor quality sequences
@FS10000436:35:BPC29621-1807:1:1101:10010:1370 2:N:0:1
GGGGGGGGGAATTTTTTTTTTTTAAAAAATATTTTTTTTTCTTTTTTTTTTTTTTTTTTCCCTTTTTTTTTTTATATTTTTTTTTTTTTTTTTATATTTTT
+
F:,,,,,,,,,,,F,,:,:FFF,,,::FF,,,,FFF,,,,,:,FFF::FF::,F::F,,,,,,,F,FF::::,,,,,,::F:FFFFFFF,F,,,,,,,,,:

I guess this problem came from library length which is shorter than sequencing length. However, I can't understand why Read2 sequence doesn't show matched short sequences (like adapter with G sequences) but random sequences. Is it cluster problems by short sequences?

Thanks in advance.

Last edited by Kujin Kwon; 11-20-2019 at 01:39 AM.
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