Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I think your approach with bowtie1 is perfectly reasonable; first clean a little all the reads (low Q, adapters...) and then filter out rRNA reads with your Porifera_rRNA database. I'm not sure about using the parameter -a/--all (instructs bowtie to report all valid alignments) along with the --un option (write all reads that could not be aligned to a file). The --best option would be work fine for cleaning rRNA reads, don't think the --strata would be necessary; you will get another fastq/fasta file with the filtered reads.
-
Personally I like bowtie2 -- the parameters can be either individually tweaked or globally tweaked via '--fast-local', '--sensitive', etc.
Leave a comment:
-
Eliminate rRNA contamination with Bowtie
Hi,
I'm working with Illumina 101bp reads of marine sponges. Before trimming the adapters and filtering by quality with the Trimmomatic i run FastQC to check, among other things, the amount of overrepresented reads to have an idea of the rRNA contamination of my raw reads. I also run FastQC after the Trimmomatic to check exactly the same thing.
Now i'm dealing with the rRNA contamination. I'm aligning my reads against all the Porifera rRNA sequences in NCBI using Bowtie with the parameter --un that keeps the unaligned reads. My logic made me do that with my already trimmed and filtered reads but maybe is better if i use as an input my 2 FASTQ paired-end (/1 and /2) raw files (without any trimming or filtering).
Also the script that i'm using is this one:
$ bowtie -a --best --strata -t --al aligned.fq --un unaligned.fq Porifera_rRNA <nameofmyfile>
I'm completely new using Bowtie so i don't know if maybe for what i'm trying to do is better to use some other parameters.
I'm looking for a little bit of feedback, i'm the only person in my lab working with that kind of stuff.
Anyone out there can help me?
Thanks.Tags: None
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
159 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Leave a comment: