What for your experience are the best parameters for short read mapping?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
I recently found another non-commercial aligner for SOLiD data - it is called subread. I have only tried for Illumina data but it's very good there.
Again, I wouldn't use tophat for such short read data.
Leave a comment:
-
I did use tophat2 with bowtie1, anyway if I let the default -g option (i think it is 20) it takes ages to finish.
As regards shrimp I didn't find any working link to download it!
Leave a comment:
-
In general, in comparison to Illumina PE reads don't expect high mapping percentages. From memory I think 50-70% was pretty good, as the data were not extensively filtered (on the 5500xl machine at least).
You probably don't want to use Tophat for such short reads as I don't think it will be able to find anchors/seeds successfully.
My best experiences with SOLiD were with the commercial program NovoalignCS. You might be able to get a free trial.
Otherwise, Shrimp2 was also not too bad.
Why not use just bowtie1 instead of tophat2 with bowtie1 ?
Leave a comment:
-
mapping 35bp solid reads with tophat unsuccessful
Hi, I recently downloaded some solid short reads (35 bp), single end, and convert them in cfasta with ahi-dump.
I found that there are very few mappers that support solid read mapping in color space and finally i decided to use tophat using bowtie1 (which supported color space mapping).
Unfortunately I less less than 30 % of the reads mapping.
My previous experience has always been with 100 bp paired end reads, so I am not completely sure if I am using the right parameters for short read mapping:
tophat -G $annotation --segment-length 17 --segment-mismatches 1 -g 1 --bowtie1 -p 12 -o $OUTPUT_FOLDER --coverage-search --color --quals $genome $READ $QUAL
maybe is the segment-mismatch and maximum multi-hits too restrictive? (-g is 20 by default). What for your experience are the best parameters for short read mapping?
Thanks
Ilario
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, 07-25-2024, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
07-25-2024, 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
160 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: