Question: filter illumina index
0
gravatar for priscilladraj
7 days ago by
priscilladraj10 wrote:

Hi, I ran an iseq illumina sequencing on my libary. And due some sample prepration problem, I have a low concentration of my libary. Hence, after sequecing and base calling, the iseq base caller grouped all my reads (dual index, 3 pooled libary = 6 reads total) under a undetermined folder. I want to know how can i still demultiplex my data that is in the undeterrminded folder? I tried using the https://pypi.org/project/filter-illumina-index/ script. BUt still cant or have I made any mistakes in my code

filter_illumina_index --1.0.4 -f FILTERED -u UNFILTERED  -i ATTACTCG -m 0 -t 1 -l 6 -v 0 /home/ubuntu/dnaread1/20200903_FS10000764_45_BPC29622-2333/Alignment_1/20200904_164251/Fastq/Undetermined_S0_L001_R1_001.fastq.gz

I thought I should demultiplex each index one by one then I can filter out my data for further analysis.

Could someone help me please. I am super new still to any demultiplxing any data

Pris

ADD COMMENTlink modified 5 days ago • written 7 days ago by priscilladraj10

Just so I can understand, could you post examples of sequences you have and a list of expected indices?

ADD REPLYlink written 6 days ago by Gabriel R.2.8k
1
gravatar for priscilladraj
5 days ago by
priscilladraj10 wrote:

thanks I manages to resolve it demultiplexing it again bcl base caller software and it worked this time because I learned that teh Iseq reads i5 from reverse complement direction. So its my mistake of not knowing this.

ADD COMMENTlink written 5 days ago by priscilladraj10
0
gravatar for genomax
7 days ago by
genomax89k
United States
genomax89k wrote:

You should demultiplex data based on solution I show here: C: demuxbyname.sh output help

There may be other unexpected index combinations present. That is normal to some extent (< 5% of total) and those can be ignored.

ADD COMMENTlink written 7 days ago by genomax89k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1547 users visited in the last hour