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

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