Hi,
I run the following command in Trimmomatic:
java -jar /home/devgen/bin/trimmomatic-0.36.jar PE -phred33 C95VLANXX-2046D-01-01-01_L003_R1.fastq C95VLANXX-2046D-01-01-01_L003_R2.fastq N6_F_P.fastq N6_F_U.fastq N6_R_P.fastq N6_R_U.fastq ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 MINLEN:25 AVGQUAL:20 -trimlog N6L3.log
Am I running it correctly?
I have RNASeq Paired end data from HiSEq2500.
The output looks like this:
TrimmomaticPE: Started with arguments:
-phred33 C95VLANXX-2046D-01-01-01_L003_R1.fastq C95VLANXX-2046D-01-01-01_L003_R2.fastq N6_F_P.fastq N6_F_U.fastq N6_R_P.fastq N6_R_U.fastq ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 MINLEN:25 AVGQUAL:20 -trimlog N6L3.log
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 16228554 Both Surviving: 12432585 (76.61%) Forward Only Surviving: 3793730 (23.38%) Reverse Only Surviving: 1926 (0.01%) Dropped: 313 (0.00%)
TrimmomaticPE: Completed successfully
---------
Is it normal to get only 76% surviving in both reads? What do I do with the upaired ones? Unpaired forward file has 23% of reads which is quiet a lot. Should I just leave this file and only use paired-survived file for alignment with tophat2?
Any advise will be greatly appreciated.
Thanks.
I run the following command in Trimmomatic:
java -jar /home/devgen/bin/trimmomatic-0.36.jar PE -phred33 C95VLANXX-2046D-01-01-01_L003_R1.fastq C95VLANXX-2046D-01-01-01_L003_R2.fastq N6_F_P.fastq N6_F_U.fastq N6_R_P.fastq N6_R_U.fastq ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 MINLEN:25 AVGQUAL:20 -trimlog N6L3.log
Am I running it correctly?
I have RNASeq Paired end data from HiSEq2500.
The output looks like this:
TrimmomaticPE: Started with arguments:
-phred33 C95VLANXX-2046D-01-01-01_L003_R1.fastq C95VLANXX-2046D-01-01-01_L003_R2.fastq N6_F_P.fastq N6_F_U.fastq N6_R_P.fastq N6_R_U.fastq ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 MINLEN:25 AVGQUAL:20 -trimlog N6L3.log
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 16228554 Both Surviving: 12432585 (76.61%) Forward Only Surviving: 3793730 (23.38%) Reverse Only Surviving: 1926 (0.01%) Dropped: 313 (0.00%)
TrimmomaticPE: Completed successfully
---------
Is it normal to get only 76% surviving in both reads? What do I do with the upaired ones? Unpaired forward file has 23% of reads which is quiet a lot. Should I just leave this file and only use paired-survived file for alignment with tophat2?
Any advise will be greatly appreciated.
Thanks.
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