Trying to trim the availavle four samples we have using this command "trimmomatic PE -threads 1 -phred33 -trimlog trimLogFile -summary statsSummaryFile $f1 $f2 $newf1 $newf1U $newf2 $newf2U \ ILLUMINACLIP:$adap/TruSeq3-PE.fa:2:30:10:1 SLIDINGWINDOW:4:15 MINLEN:36" and it didn't work

[ZainabKamel]

We figured out it didn't work with us because we are not working on paired end reads

[ZainabKamel]

We then added to it trimmomatic SE -phred33 ~/Desktop/PROJECT/SAMPLE_DATA/hs_T47D_shCTRL_RNAseq_rep1.fastq.gz results.fq.gz ILLUMINACLIP:TRUSeq-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:13 CROP:61

[ZainabKamel]

The last command allowed us to crop the bases with problems from the start and end

[Hadeeribrahiem173]

After looking at the QC report, we get the best parameters to modify our data that are mentioned above in the command after trying the parameters in Galaxy which are:

Adapter sequences to use

Maximum mismatch count which will still allow a full match to be performed=2 How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment=30 How accurate the match between any adapter etc. sequence must be against a read=10 Minimum length of adapter that needs to be detected (PE specific/palindrome mode)=8

SLIDING WINDOW

Number of bases to average across=4 Average quality required=15

LEADING

Minimum quality required to keep a base=3

TRAILING

Minimum quality required to keep a base=3

MINLEN

Minimum length of reads to be kept=36

HEADCROP

Number of bases to remove from the start of the read=13

CROP

Number of bases to keep from the start of the read=61