Do the default parameters of Bowtie2 (sensitive: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)) provide good enough results to publish for assembling Illumina HiSeq unpaired 101 bp reads to a reference chloroplast genome? I don't know how to change parameters and wouldn't know what to change them to even if I could. The default parameters seem to be giving good results. Any suggestions?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
It kind of depends on the question you are trying to answer. obviously. But I would say the answer is yes, there's no pressing need to change the params unless you have a specific reason to. It's fairly key to know the % of reads that have mapped successfully, and it's also worth examining the alignment (e.g. samtools tview or a windowed viewer like Tablet) to check there are no obvious misalignments.
Latest Articles
Collapse
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:55 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:55 AM
|
||
Started by seqadmin, 05-30-2024, 03:16 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
05-30-2024, 03:16 PM
|
||
Comprehensive Sequencing of Great Ape Sex Chromosomes Yields Insights into Evolution and Genetic Variability
by seqadmin
Started by seqadmin, 05-29-2024, 01:32 PM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
05-29-2024, 01:32 PM
|
||
Started by seqadmin, 05-24-2024, 07:15 AM
|
0 responses
215 views
0 likes
|
Last Post
by seqadmin
05-24-2024, 07:15 AM
|
Comment