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<center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_1.png"/> <br> </center> |
Workflow Wizard
The wizard for singleworkflows have the similar wizards. The wizard for paired-end reads has 5 page.
Input data: On On this tab page you need to must input the FASTQ files, obtained from the sequencer. One or several files can be specified as input.FASTQ file(s).
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_27.png"/> <br> </center>
Pre-processing: On this tab there are parameters for sequencing reads trimming and the default file with adapter sequences that should be cut. On this page you can modify filtration parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_38.png"/> <br> </center>
The following parameters are available:
Quality threshold – trim all bases with quality score lower than the value of the parameter.
Min length – the minimum length of a trimmed read.
Adapters – the list of adapter sequences to be trimmed by the cutadapt tool
Base quality Quality threshold for trimming. Reads length Too short reads are discarded by the filter. Trim both ends Trim the both ends of a read or not. Usually, you need to set True for Sanger sequencing and False for NGS Base quality for pairs
Quality threshold for trimming. Reads length for pairs
Too short reads are discarded by the filter. Trim both ends for pairs
Trim the both ends of a read or not. Usually, you need to set True for Sanger sequencing and False for NGS Adapters
A FASTA file with one or multiple sequences of adapter that were ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$ character, the adapter is anchored to the end of the read and only found if it is a suffix of the read. Adapters for pairs
A FASTA file with one or multiple sequences of adapter that were ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$ character, the adapter is anchored to the end of the read and only found if it is a suffix of the read.
Mapping: On this page you must input reference and optionally modify advanced parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_49.png"/> <br> </center>
Post-processing: On this page you can modify post-processing parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_5.png"/> <br> </center>Output data: On this page you must input output parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_6.png"/> <br> </center>
The wizard for paired-end reads has 5 page.
Input data: On this page you must input FASTQ file(s).
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_7.png"/> <br> </center>Pre-processing: On this page you can modify filtration parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_8.png"/> <br> </center>Mapping: On this page you must input reference and optionally modify advanced parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_9.png"/> <br> </center>The following parameters are available:
Reference genome Path to indexed reference genome. Number of threads Number of threads (-t). Min seed length Path to indexed reference genome (-k). Band width
Band width for banded alignment (-w).
Dropoff
Off-diagonal X-dropoff (-d).
Internal seed length
Look for internal seeds inside a seed longer than {-k} (-r).
Skip seed threshold
Skip seeds with more than INT occurrences (-c).
Drop chain threshold
Drop chains shorter than FLOAT fraction of the longest overlapping chain (-D).
Rounds of mate rescues Perform at most INT rounds of mate rescues for each read (-m). Skip mate rescue Skip mate rescue (-S). Skip pairing Skip pairing; mate rescue performed unless -S also in use (-P). Mismatch penalty Score for a sequence match (-A). Mismatch penalty Penalty for a mismatch (-B). Gap open penalty Gap open penalty (-O). Gap extention penalty Gap extension penalty; a gap of size k cost {-O} (-E). Penalty for clipping Penalty for clipping (-L). Penalty unpaired Penalty for an unpaired read pair (-U). Score threshold Minimum score to output (-T). Post-processing: On this page you can modify post-processing parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_10.png"/> <br> </center>
The following parameters are available:
MAPQ threshold Minimum MAPQ quality score. Skip flag Skip alignment with the selected items. Select the items in the combobox to configure bit flag. Do not select the items to avoid filtration by this parameter. Region Regions to filter. For BAM output only. chr2 to output the whole chr2. chr2:1000 to output regions of chr 2 starting from 1000. chr2:1000-2000 to ouput regions of chr2 between 1000 and 2000 including the end point. To input multiple regions use the space seprator (e.g. chr1 chr2 chr3:1000-2000). For single-end reads
Remove duplicates for single-end reads.
Output data: On this page you must input output parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122726/Raw DNA-Seq Processing_11.png"/> <br> </center>
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