My problem is having shorter fragments after sequencing than expected. The size of my library should be around 300 bp and I checked the size with Tape station which was ~300 bp. However, my sequencing results show that my actual transcripts are too short that that even can`t be mapped to anywhere. Then, I checked my libraries with Sanger sequencing and they were also around 150 bp.
What can it be the reason that I see at Tape station results that 300-350 bp but our fragments are less than 150??
The only mistake I am sure is my libraries (CEL-Seq libraries, which you can pool many samples in one tube) is not compatible with Hi-Seq v4 chemistry (don`t know the reason but the method published to be so, now the authors says it works with v4 only %20 Phix is used) but works fine with v3 chemistry or Rapid mode. Previously the same protocol worked fine with Rapid mode and now we tried v4 with %1 Phix and the results are very strange with short fragments.
Any idea??
What can it be the reason that I see at Tape station results that 300-350 bp but our fragments are less than 150??
The only mistake I am sure is my libraries (CEL-Seq libraries, which you can pool many samples in one tube) is not compatible with Hi-Seq v4 chemistry (don`t know the reason but the method published to be so, now the authors says it works with v4 only %20 Phix is used) but works fine with v3 chemistry or Rapid mode. Previously the same protocol worked fine with Rapid mode and now we tried v4 with %1 Phix and the results are very strange with short fragments.
Any idea??
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