Should I use the masked genome or not (chromFaMasked vs. chromFa; both from UCSC) to align my chIP-seq data? If it depends on the alignment programs? Thanks!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I would think this would depend on the aligner you're using, and what you plan to do with multi-match reads.
Depending on what you've precipitated in your ChIP, You're probably more interested in unique regions, anyhow, so I don't think it will make a big difference for the most part. If you were working with whole genome or wtss, I would expect it to have a bigger impact.The more you know, the more you know you don't know. —Aristotle
-
Definitely unmasked. The repeats masked by repeatmasker (alu, line, sine, mir etc) do contain unque sequences, and probably using masked reference would lead to false alignments of reads from repeats if you allow several mismatches. chr.fa files are also repeatmasked but to lowercase rather than N:s so this information can still be used by some aligners-
Comment
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 03-27-2024, 06:37 PM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:37 PM
|
||
Started by seqadmin, 03-27-2024, 06:07 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
69 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment