Hi Everybody,
I wondered if I could ask a question regarding bowtie2
I'm trying to align around 500 samples of PE data to a reference genome producing a .sam file output for each.
I've tried running specifying:
bowtie2 -x assembly44indexfile -1 *.1.fq.gz -2 *.2.fq.gz -S (but this aligns all input reads into a single SAM)
I've tried running specifying:
bowtie2 -x assembly44indexfile -1 ind1.1.fq.gz,ind2.1.fq.gz -2 ind1.2.fq.gz,ind2.2.fq.gz -S (but again all samples get aligned in a single SAM)
I've tried running a script I found on the net and altered to the below but it didn't run (I'm slightly lost on writing scripts:
for sample in `ls /data/omicsScratch/mpx247/script/rad`
do
dir="/data/omicsScratch/mpx247/script/rad"
base=$(basename $sample ".1.fq.gz")
bowtie2 -x /data/omicsScratch/mpx247/script/rad/assembly44indexfile -1 ${dir}/${base}.1.fq.gz -2 ${dir}/${base}.1.fq.gz -S$
done
I wonder if anybody knows an answer at all or can offer advice as to how to deal with this issue. All my read 1's end in .1.fq.gz and read 2's .2.fq.gz with a prefix of usually something like AU12 (sample 12 from Australia) but sometimes this has additional info in the prefix.
Thanks so much for any help
Best
J
See if this works.
Please help me?
I want to learn bowtie2 but some trouble ...
Could not locate a Bowtie index corresponding to basename "/home/otgoo/jishee/amplicons_dk.fa" Error: Encountered internal Bowtie 2 exception (#1) Command: /usr/bin/../lib/bowtie2/bin/bowtie2-align-s --wrapper basic-0 -p16 -x /home/otgoo/jishee/amplicons_dk.fa -s /home/otgoo/jishee/result/dun.sam -1 /home/otgoo/jishee/VEGF1_S1_L001_R1_001.fastq -2 /home/otgoo/jishee/VEGF1_S1_L001_R2_001.fastq (ERR): bowtie2-align exited with value 1
My input is "bowtie2 -p16 -x /home/otgoo/jishee/amplicons_dk.fa -1 /home/otgoo/jishee/VEGF1_S1_L001_R1_001.fastq -2 /home/otgoo/jishee/VEGF1_S1_L001_R2_001.fastq -s /home/otgoo/jishee/result/dun.sam"
Have you created the bowtie2 indexes by using the command
bowtie2-build
? If not you should do that first.bowtie2-build -f your_fasta my_index
(something along this line). Then usemy_index
as the base name for the index.Thanks for your reply. Yes I have created indexes files (there, 6 files were created) by bowtie2-build.
Can you provide the
bowtie2-build
command that you used? Is the amplicons_dk.fa file in the same directory as the other six index files?Ok. I used following command.
bowtie2-build /home/otgoo/example/reference/lambda_virus.fa /home/otgoo/example/index/index.fasta
That means you set the "base name" for your index to
index.fasta
. So you would need to run your command asOk. That is working thank you very much. In future, Could I ask to you for some question on these study ? Best regards.
Sure. If the new question is unrelated to the original in this thread you can start a new post.