Question: "View Details" Of Tophat Alignment
0
Du, Jianguang • 110 wrote:
Hi All,
After I finshed Tophat alignment for RNA-seq, I took look at the
details of parameters by clicking the icon "View details", and I got
the information as shown below:
Input Parameter Value Note for rerun
RNA-Seq FASTQ file 73: Filtered Groomed data1_rep2
Use a built in reference genome or own from your history
indexed
Select a reference genome /galaxy/data/mm9/bowtie_index/mm9
Is this library mate-paired? single
TopHat settings to use full
Library Type FR Unstranded
Anchor length (at least 3) None
Maximum number of mismatches that can appear in the anchor region of
spliced alignment None
The minimum intron length None
The maximum intron length None
Allow indel search No
Maximum number of alignments to be allowed None
Minimum intron length that may be found during split-segment (default)
search None
Maximum intron length that may be found during split-segment (default)
search None
Number of mismatches allowed in the initial read mapping None
Number of mismatches allowed in each segment alignment for reads
mapped independently None
Minimum length of read segments None
Use Own Junctions Yes
Use Gene Annotation Model Yes
Gene Model Annotations 1: mm9 genes.gtf
Use Raw Junctions No
Only look for supplied junctions No
Use Closure Search No
Use Coverage Search Yes
Minimum intron length that may be found during coverage search None
Maximum intron length that may be found during coverage search None
Use Microexon Search No
I am totally confused by so many "None"s.
Then I checked the workflow I set and used for the TopHat alignment,
the details are the same as above.
However, the brief description just under the title of alignment
output (. accepted hits) is as below:
format: bam, database: mm9
Tophat for Illumina on data 1 and data 73: accepted_hits, TopHat
v1.4.0 tophat -p 8 -a 8 -m 0 -i 70 -I 500000 -g 20 -G
/galaxy/main_pool/pool1/files/004/425/dataset_4425972.dat --library-
type fr-unstranded --no-novel-indels --coverage-search --min-cove
Could you please tell me is there anything wrong (because so many
"None" in the detail parameters)?
Thanks.
Jianguang DU
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modified 5.5 years ago
by
Jeremy Goecks • 2.2k
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written
5.5 years ago by
Du, Jianguang • 110
