Changes between Version 58 and Version 59 of SOPs/mapping

Timestamp:

02/26/18 12:33:45 (7 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -160 +160 @@
 bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq /path/to/read2.fastq --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8
 # Input format: fastq.gz ; output format: BAM (sorted by position)
-bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
 
 #mapping when gtf/overhang was not specified during indexing
-bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang readLength-1
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang readLength-1
 
 }}}
@@ -174 +174 @@
   * '''--sjdbScore <n> ''' Provides extra alignment score for alignments that cross database junctions (default = 2). If this score is positive, it will bias the alignment toward annotated junctions. This is only used if during the genomeGenerate step a splice junction annotation file is used.  
   * '''--runThreadN <n> ''' Specifies the number of threads to use.
-  * '''--readFilesCommand <cmd> ''' Specifies the command to uncompress compressed fastq files. For gzipped files (*.gz) use --readFilesCommand gunzip -c.
+  * '''--readFilesCommand <cmd> ''' Specifies the command to uncompress compressed fastq files. For gzipped files (*.gz) use --readFilesCommand zcat.
   * '''--outSAMtype <BAM sortingMode> ''' Specifies the type of BAM file to create.  Options: 'BAM Unsorted', 'BAM SortedByCoordinate', 'BAM Unsorted SortedByCoordinate' (to create both unsorted and sorted BAMs)