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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