Question: Remove or keep the overdispersed reads in Single cell RNA seq analysi
0
gravatar for hemantcnaik
3 months ago by
hemantcnaik0 wrote:

Hello I am working on single cell in my data fastqc showing overdispersed read as below I have to remove this sequences or not can anyone suggest me

if yes how can I remove please mention tools related

                                  Sequence     Count    Percentage       Possible Source
 TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTT    13087   0.48103129699078845 No Hit
 GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTT    6111    0.2246184959051508  No Hit
 GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTT    5368    0.19730847422988865 No Hit
ADD COMMENTlink modified 3 months ago • written 3 months ago by hemantcnaik0

What platform is this single cell sequencing data from? Generally if this is 10x then it cellranger software will take care of eliminating/soft-clipping the data during alignment.

ADD REPLYlink written 3 months ago by GenoMax92k

Thanks for your reply, Illumina HiSeq 2500 squencer

ADD REPLYlink modified 3 months ago • written 3 months ago by hemantcnaik0
1

genomax was asking about the type of library (e.g. 10x, Smart-Seq, InDrop, MARS...), not the sequencer. Anyway, the percentages of these overrepresented sequences are tiny. I would ignore it and proceed with analysis.

ADD REPLYlink written 3 months ago by ATpoint42k

Thank you for your reply.

ADD REPLYlink written 3 months ago by hemantcnaik0
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