5' bias

Hello

I got a strong 5' bias. First positions in a transcript have a high( very high coverage) . The window that follows has almost no reads.

I believe the figure should speak for itself. I join also the parameters file used.

Any suggestions on how to reduce this bias?

Thank you,

Bogdan

5bias.png

PARAMETER TABLE:

NB_MOLECULES     50000

TSS_MEAN    NaN

POLYA_SCALE    50

POLYA_SHAPE     2

## Fragmentation

FRAG_SUBSTRATE  RNA

FRAG_METHOD     UR

FRAG_NB_LAMBDA 50

## RT parameters

RTRANSCRIPTION YES

RT_PRIMER      RH

RT_LOSSLESS    YES

RT_MIN        2000

RT_MAX        6000

## PCR / Filtering

## no [GC] bias to not observe sequence based biases

PCR_DISTRIBUTION  default

PCR_PROBABILITY 0.5

GC_MEAN NaN

FILTERING         YES

SIZE_SAMPLING     MH

# Sequencing

FASTA    true

READ_NUMBER     1000000

READ_LENGTH     50

PAIRED_END      NO