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Hello,
I am trying to analyze a few SOLiD samples with miRDeep2 in order to find known/novel microRNAs.
The raw reads are all 35 nt long and miRDeep2 requires the 3' adapter sequence in order to trim it.
LifeTech support has provided me with the Internal Adapter sequence CGCCTTGGCCGTACAGCAG, but I was only able to trim 0.1% of reads by using cutadapt and 8% of them by using the Clip adapter sequence on Galaxy.
When I provided miRDeep2 with that sequence it was able to map very few reads, so this makes me think that the adapter sequence is not correct.
I don't know if this helps, but here are some information on the kit used:
NEBNext Small RNA Library Prep Set for SOLiD (NEB cat. no. E6160)
SOLiD™ RNA Barcoding Kit, Modules 1-16 (Ambion cat. no. 4427046)
SOLiD™ RNA Barcoding Kit, Modules 17-32 (Ambion cat. no. 4453189)
Does anyone have any clue what the problem is and/or how I can get the correct adapter sequence?
I am trying to analyze a few SOLiD samples with miRDeep2 in order to find known/novel microRNAs.
The raw reads are all 35 nt long and miRDeep2 requires the 3' adapter sequence in order to trim it.
LifeTech support has provided me with the Internal Adapter sequence CGCCTTGGCCGTACAGCAG, but I was only able to trim 0.1% of reads by using cutadapt and 8% of them by using the Clip adapter sequence on Galaxy.
When I provided miRDeep2 with that sequence it was able to map very few reads, so this makes me think that the adapter sequence is not correct.
I don't know if this helps, but here are some information on the kit used:
NEBNext Small RNA Library Prep Set for SOLiD (NEB cat. no. E6160)
SOLiD™ RNA Barcoding Kit, Modules 1-16 (Ambion cat. no. 4427046)
SOLiD™ RNA Barcoding Kit, Modules 17-32 (Ambion cat. no. 4453189)
Does anyone have any clue what the problem is and/or how I can get the correct adapter sequence?
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