Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I sometimes use bowtie2 for the alignment stage of running RSEM (RNA-Seq gene expression). RSEM didn't allow INDELS in the alignments so as part of tweaking bowtie2 to not report those I was advised to set '--dpad 0'.
-
Sorry the first explanation I posted was from bowties implemented command line help. The following description was actually taken from the manual:
--dpad <int>
“Pads” dynamic programming problems by <int> columns on either side to allow gaps. Default: 15.
Leave a comment:
-
bowtie 2 dpad parameter explanation
Can someone provide a detailed explanation, what the bowtie2 parameter "--dpad" does? The explanation given in the manual is as follows: "--dpad <int> include <int> extra ref chars on sides of DP table (15)".
I would interprete it like this:
1) A sequence string of length <int> is attached to every 5' and 3' end of a read after seeding and global alignment.
2) Attached sequences are used to solve mapping issues at readends (e.g. deletions present at readends that have been falsley softclipped in previous steps).
!!!But I am really not confident with this!!!
I am asking because I realised that increasing dpad to an integer of 100, solves issues I have to face with large deletions in a merged 350bp Illumina amplicon dataset. I mean solving this issue is fine, but I do not have a clue what the possible drawbacks of this setting might be. Furthermore, as I do not exactly understand the parameter and its behaviour, I do not know how to test for possible side-effects.
Here are my option settings:
bowtie2 --rdg 5,1 --rfg 5,1 --dpad 100 --score-min L,0,-0.75 --very-sensitive
Latest Articles
Collapse
-
by seqadmin
Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.
Nucleic Acid Quality Control
Preparing for NGS starts with isolating the...-
Channel: Articles
02-10-2025, 01:58 PM -
-
by seqadmin
In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...-
Channel: Articles
01-27-2025, 07:46 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Genetic Mapping of Plasmodium knowlesi Identifies Essential Genes and Drug Resistance Mechanisms
by seqadmin
Started by seqadmin, 02-07-2025, 09:30 AM
|
0 responses
54 views
0 likes
|
Last Post
by seqadmin
02-07-2025, 09:30 AM
|
||
Started by seqadmin, 02-05-2025, 10:34 AM
|
0 responses
88 views
0 likes
|
Last Post
by seqadmin
02-05-2025, 10:34 AM
|
||
Started by seqadmin, 02-03-2025, 09:07 AM
|
0 responses
70 views
0 likes
|
Last Post
by seqadmin
02-03-2025, 09:07 AM
|
||
Started by seqadmin, 01-31-2025, 08:31 AM
|
0 responses
44 views
0 likes
|
Last Post
by seqadmin
01-31-2025, 08:31 AM
|
Leave a comment: