Changes between Version 42 and Version 43 of SOPs/mapping
- Timestamp:
- 04/26/17 11:03:39 (8 years ago)
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SOPs/mapping
v42 v43 6 6 It's thoroughly described in the [[http://www.ncbi.nlm.nih.gov/books/NBK47528/|SRA Handbook]] 7 7 8 Processing SRA files requires the [[https:// tak.wi.mit.edu/trac/wiki/sra-toolkit|NCBI SRA Toolkit]], which is installed on our systems.8 Processing SRA files requires the [[https://ncbi.github.io/sra-tools/|NCBI SRA Toolkit]], which is installed on our systems. 9 9 10 10 The main command is **fastq-dump <SRA archive file>**, like … … 20 20 ''**fastq-dump --gzip SRR060751.sra**'' 21 21 22 See [[http ://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.5_Converting_SRA_for|Converting SRA format data into FASTQ]] for all program options.22 See [[https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump|Converting SRA format data into FASTQ]] for all program options. 23 23 24 24 Note that a fastq file is about 4-5x larger than its corresponding SRA file. … … 136 136 These mappers permit the beginning and end of a read to map to (originate from) different places in the genome, which is common for spliced RNA. 137 137 138 ''' [http://tophat.cbcb.umd.edu/ tophat version 1]'''138 '''tophat version 1 (old)''' 139 139 140 140 Running TopHat version 1 requires a change to a user's environment on tak and only applies to the specific tak session. First run this command: … … 163 163 * '''--solexa1.3-quals''' or '''--phred64-quals''' (for input quality scores from Illumina versions 1.3-1.7) 164 164 165 '''[http:// tophat.cbcb.umd.edu/tophat version 2]'''165 '''[http://ccb.jhu.edu/software/tophat/index.shtml tophat version 2]''' 166 166 167 167 TopHat version 2 uses bowtie2, rather than bowtie, for its mapping. As a result, TopHat 2 uses a different set of genome index files (*.bt2) than TopHat 1 (*.ebwt).
