Question: Bowtie2 error RNA seq aligning to genome
0
gravatar for nidhi.vijayan13
10 months ago by
nidhi.vijayan1320 wrote:

I first used Trimmomatic using the command:

java -jar $Trimmomatic PE ~/transcriptome/WT_LO2_1.fastq ~/transcriptome/WT_LO2_2.fastq ~/transcriptome/trimmed/WT_LO/WT_LO2_forward.fq.gz ~/transcriptome/trimmed/WT_LO/WT_LO2_reverse.fq.gz ILLUMINACLIP:TruSeq3-PE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50

I tried it with and without "keepbothreads" option. Both times I got 10x more forward reads than reverse

Then when I use bowtie to map to the genome using the script:

bowtie2 -x host_DB -1 ~/transcriptome/trimmed/WT_LO/WT_LO1_forward.fastq -2 ~/transcriptome/trimmed/WT_LO/WT_LO1_reverse.fastq -S WT_LO1_mapped_and_unmapped.sam

It starts the process and I get an output file, but it stops with an error: Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT)

rna-seq alignment assembly • 260 views
ADD COMMENTlink modified 10 months ago by genomax89k • written 10 months ago by nidhi.vijayan1320

You can try repair.sh from BBMap suite to re-sync paired end reads in the two files and remove singletons.

Since you did trim your data files together I suggest going back to the original data files and repairing those files before doing the trimming. I suspect your original files are not in sync.

ADD REPLYlink written 10 months ago by genomax89k
0
gravatar for nidhi.vijayan13
10 months ago by
nidhi.vijayan1320 wrote:

I fixed it by using the following script:

java -jar $Trimmomatic PE ~/transcriptome/WT_LO2_1.fastq ~/transcriptome/WT_LO2_2.fastq LO2_forward_paired.fq.gz LO2_forward_unpaired.fq.gz LO2_reverse_paired.fq.gz LO2_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE:2:30:10:2:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50

The repair.sh script did not work for my files.

ADD COMMENTlink written 10 months ago by nidhi.vijayan1320
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1164 users visited in the last hour