Hi,
I would like to remove the adapters from a RNA-seq reads of many studies. I download the reads from GEO NCBI. In some case, the sequence adapter is specified (sometime I have to go through the paper) and in other they are not specified at al.
e.g. http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1918965
Here for instance, I tried to this adaper CTGTAGGCACCATCAAT with this fastx_clipper
fastx_clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -v -z -n
However, it seems that it is not the good adapter since only 15,000 reads are remaning.
Is there a way to find the sequence adapter when not specify in the study and without spending time to go through the paper?
(I am ok to use any other software like cutadapt etc..)
Thanks
I would like to remove the adapters from a RNA-seq reads of many studies. I download the reads from GEO NCBI. In some case, the sequence adapter is specified (sometime I have to go through the paper) and in other they are not specified at al.
e.g. http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1918965
Here for instance, I tried to this adaper CTGTAGGCACCATCAAT with this fastx_clipper
fastx_clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -v -z -n
However, it seems that it is not the good adapter since only 15,000 reads are remaning.
Is there a way to find the sequence adapter when not specify in the study and without spending time to go through the paper?
(I am ok to use any other software like cutadapt etc..)
Thanks
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