I have tried to use flux simulation
tool to generate simulated RNA-seq data.
I gave the following parameter file to flux-simulation shell script
## File locations
REF_FILE_NAME cElegansAnnotation.gtf
GEN_DIR chromFa
## Library preparation
# Expression
NB_MOLECULES 5000000
TSS_MEAN 50
POLYA_SCALE 100
POLYA_SHAPE 1.5
# Fragmentation
FRAG_SUBSTRATE RNA
FRAG_METHOD UR
FRAG_UR_ETA 350
# Reverse Transcription
RTRANSCRIPTION YES
RT_MOTIF default
# Amplification
PCR_DISTRIBUTION default
GC_MEAN NaN
PCR_PROBABILITY 0.05
# Size Filtering
FILTERING NO
## Sequencing
READ_NUMBER 1000000
READ_LENGTH 100
PAIRED_END YES
# create a fastq file
FASTA YES
According to this parameter, flux-simulation should have given reads with length 100. However when I look at the output, I have seen that reads with less then length of 100 are also included in my fasta file:
>chrI:47472-49416W:Y48G1C.12:3:651:351:594:A/1
CGTCGAAATTAGTGATATTTTTATCGGGAATCGGTCCGTGTGGTTCTCCGGTGAATATTCGATTCGTTGTGGAGACACGAGATCGCTGGGGTCCAAGGAC
>chrI:47472-49416W:Y48G1C.12:4:651:394:467:S/1
TACGCGACAAAAATGGGAAACCGAATCGCGTTTTTTGGCTTCAAGTACAAGTTATTCAGAATCATCAAAATGGG
>chrI:47472-49416W:Y48G1C.12:4:651:394:467:A/2
CCCATTTTGATGATTCTGAATAACTTGTACTTGAAGCCAAAAAACGCGATTCGGTTTCCCATTTTTGTCGCGTA
>chrI:47472-49416W:Y48G1C.12:5:651:126:142:S/2
AGTTGTAAAAGCGGATT
So, is there anyone how could I fix it?
awk 'NR%2==1{h=$0} (NR%2==2) && (length($0)>x){print h"\n"$0}' fastafile.fa
$\endgroup$