Question: how to prepare a contaminant list for Bowtie2
0
gravatar for jolin0701-dy
4.3 years ago by
jolin0701-dy70
jolin0701-dy70 wrote:

I'd like to prepare a contaminant list to filter contaminant reads mapped to mitochondrial, ribosomal, actin RNA or phi X genomes28 bu Bowtie2.

Where can I download these sequeces for human and mouse?

Since it is the common contaminant, any available fasta files or bowtie index files for them?

Thanks~~

rna-seq • 1.9k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by jolin0701-dy70

removed rRNA tRNA in arabidopsis (using bowtie2)

ADD REPLYlink written 4.3 years ago by fanli.gcb690

Why do you want to filter those reads? Depending on the GTF file you use for read summarization reads that align to any/all of these would not be counted since you can exclude these features/meta-features from that GTF file.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by genomax85k
1
gravatar for jolin0701-dy
4.3 years ago by
jolin0701-dy70
jolin0701-dy70 wrote:

I ran the index for phiX.

Then I want to run bowtie2 to exclude the sequences from fastq file.

./YZ1_S1_L001_R1_001.cuttrimmed.fastq is my input file.

./contam/phiX/phiX_index is the path to index

./nophiX.fastq is the output file exclude the phiX sequences.

$bowtie2 --un=./nophiX.fastq ./contam/phiX/phiX_index ./YZ1_S1_L001_R1_001.cuttrimmed.fastq

But the output file is 0kb and nothing is running.

Something wrong with the command?

Thanks….

ADD COMMENTlink written 4.3 years ago by jolin0701-dy70

You may want to look at BBSplit from BBMap suite. This would be a much better tool for what you are trying to do and you can do all decontamination in one step.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by genomax85k

The order of parameters is important in case of most tuxedo suite programs (bowtie2 is one of them). Also lookup the correct parameters before using them.
Try

$ bowtie2 -x ./contam/phiX/phiX_index ./YZ1_S1_L001_R1_001.cuttrimmed.fastq --un ./nophiX.fastq
ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by genomax85k

I used it and shows

Error: Must specify at least one read input with -U/-1/-2 (ERR): bowtie2-align exited with value 1

Any thoughts?

Thanks~~

ADD REPLYlink written 4.3 years ago by jolin0701-dy70

I have corrected bowtie2 command line above. Try the new one now. Sorry about that.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by genomax85k

Thanks, it works.

Would you tell me how to run it in background and check the status of the running??

ADD REPLYlink written 4.3 years ago by jolin0701-dy70
1
$ bowtie2 -x ./contam/phiX/phiX_index ./YZ1_S1_L001_R1_001.cuttrimmed.fastq --un ./nophiX.fastq &

Note the & at the end of the command that puts the job in the background. Do not close the terminal you start this from. If you look at a real time process monitor ($ top) you should be able to see the job running.

ADD REPLYlink written 4.3 years ago by genomax85k
0
gravatar for jolin0701-dy
4.3 years ago by
jolin0701-dy70
jolin0701-dy70 wrote:

I downloaded phiX genomes from NCBI and save it as phiX.fa

Then I ran bowtie2-build and got an error.

$ bowtie2-build phiX.fa phiX

Traceback (most recent call last):

File "/usr/local/bin/bowtie2-build", line 95, in <module> main()

File "/usr/local/bin/bowtie2-build", line 92, in main os.execv(build_bin_spec, argv)

OSError: [Errno 2] No such file or directory

Would someone tell me what's wrong with it?

Thanks~~

ADD COMMENTlink written 4.3 years ago by jolin0701-dy70

Please use a different name for the index to avoid confusion with fasta file later on. See if the following works.

$ bowtie2-build ./phiX.fa phiX_indx

phiX_indx will become the basename of the index.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by genomax85k
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: 1505 users visited in the last hour