Here is a problem when processing CshlShortRnaSeq data from ENCODE.
For example, for 1*36bp Gm12878, I found the adaptor or primer sequence of small RNA library were:
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5’SBS3_Adapter (This is the RNA ligated onto the 5’ end): “r” = ribose, RNA base
5’- rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU
A-Tail RT Primer (This is the primer used in the RT reaction):
5’-TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTTTTTTTTTTTVN
PE 5’ PCR (PCR Primer):
5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC
PE 3’ PCR (PCR Primer):
5’-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTC
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but I found that there were few reads with the adaptor on the 5' side, but rather, there are many "AGATCGGTTGT*" (the reverse of 5'adaptor) after the ployA in the 3' side. So, I am not sure if it would be correct if I clip the 5'SBS3_adaptor and 3'ploy A, and process those data accuratly using aligners such as Bowtie.
I will be appreciative if anyone could help~
For example, for 1*36bp Gm12878, I found the adaptor or primer sequence of small RNA library were:
-------------------------------------------------------------------
5’SBS3_Adapter (This is the RNA ligated onto the 5’ end): “r” = ribose, RNA base
5’- rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU
A-Tail RT Primer (This is the primer used in the RT reaction):
5’-TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTTTTTTTTTTTVN
PE 5’ PCR (PCR Primer):
5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC
PE 3’ PCR (PCR Primer):
5’-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTC
----------------------------------------------------------------------
but I found that there were few reads with the adaptor on the 5' side, but rather, there are many "AGATCGGTTGT*" (the reverse of 5'adaptor) after the ployA in the 3' side. So, I am not sure if it would be correct if I clip the 5'SBS3_adaptor and 3'ploy A, and process those data accuratly using aligners such as Bowtie.
I will be appreciative if anyone could help~
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