Galaxy | Accessible Workflow | Map Illumina Indiv. to candidate transcripts and count

Map Illumina Indiv. to candidate transcripts and count

Step	Annotation
Step 1: Map with Bowtie for Illumina Will you select a reference genome from your history or use a built-in index? Use one from the history Select the reference genome select at runtime Choose whether to use Default options for building indices or to Set your own Default Is this library mate-paired? Single-end FASTQ file select at runtime Bowtie settings to use Full parameter list Skip the first n reads (-s) 0 Only align the first n reads (-u) -1 Trim n bases from high-quality (left) end of each read before alignment (-5) 0 Trim n bases from low-quality (right) end of each read before alignment (-3) 0 Alignment mode Maq-like: quality-aware, limit mismatches in seed (-n) Maximum number of mismatches permitted in the seed (-n) 2 Maximum permitted total of quality values at all mismatched read positions (-e) 70 Seed length (-l) 28 Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround) Round to nearest 10 Choose whether or not to attempt to align against the forward reference strand (--nofw) Align against the forward reference strand Choose whether or not to attempt to align against the reverse-complement reference strand (--norc) Align against the reverse-complement reference strand Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best) Use best Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata) Do not use strata option Whether or not to try as hard as possible to find valid alignments when they exist (-y) Do not try hard Maximum number of backtracks permitted when aligning a read (--maxbts) 800 Whether or not to report all valid alignments per read (-a) Do not report all valid alignments Report up to n valid alignments per read (-k) 1 Suppress all alignments for a read if more than n reportable alignments exist (-m) -1 Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max) False Write all reads that could not be aligned to a file (--un) False Override the offrate of the index to n (-o) -1 Seed for pseudo-random number generator (--seed) -1 Save the bowtie mapping statistics to the history False No value found for 'Save the bowtie mapping statistics to the history'. Using default: 'False'. Suppress the header in the output SAM file (--sam-nohead) False Job Resource Parameters Use default job resource parameters
Step 2: SAM-to-BAM Choose the source for the reference genome Use a genome from the history SAM file to convert Output dataset 'output' from step 1 Using reference file select at runtime Job Resource Parameters Use default job resource parameters
Step 3: BAM Index Statistics BAM dataset to generate statistics for Output dataset 'output1' from step 2
Step 4: SAM/BAM Alignment Summary Metrics SAM/BAM dataset to generate statistics for Output dataset 'output1' from step 2 Title for the output file Picard Alignment Summary Metrics Select Reference Genome Use a genome (fasta format) from my history Select a reference genome from history select at runtime Assume the input file is already sorted True Input file contains Bisulphite sequenced reads False Adapter sequences Empty. Larger paired end reads and inter-chromosomal pairs considered chimeric 100000

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ts-ecogen

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