Changes between Version 65 and Version 66 of SOPs/mapping

Timestamp:

08/04/20 06:31:57 (4 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -13 +13 @@
 Sample command:
 {{{
-bsub bowtie  -k 1 -n 2 -l 70 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt s7_mm9.k1.n2.l36.best.sam
+bsub bowtie  -k 1 -n 2 -l 50 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 Sample_A.fq Sample_A.mm9.k1.n2.l50.best.sam
 }}}
 
 Parameters included in the sample command:
-  * '''-l/--seedlen <int>'''     seed length for -n (default: 28) -- Set to longest possible length of high-quality bases.  Use the FastQC output to determine length of high-quality positions.
+  * '''-l/--seedlen <int>'''     seed length for -n (default: 28) -- Set to longest possible length of high-quality bases (but no longer than 40-50, or mapping may become too stringent).  Use the FastQC output to determine length of high-quality positions.
   * '''-n/--seedmms <int>'''     max mismatches in seed (can be 0-3, default: -n 2)
   * '''-k <int>'''               report up to <int> good alignments per read (default: 1) -- If you want only uniquely mapped reads, however, also use '-m 1' to ignore multi-mapped reads; use --all to report all alignments (much slower, ie. turn-off -k option)
@@ -37 +37 @@
 Sample command:
 {{{
-bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 -U s_7.txt -S s7_mm9.L22.N1.sam
+bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 -U Sample_A.fq -S Sample_A.mm9.L22.N1.sam
 }}}
 
@@ -95 +95 @@
 '''[https://github.com/alexdobin/STAR STAR]'''
 
-STAR ([https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf manual]) is an ultrafast universal RNA-seq aligner.  It maps >60 times faster than Tophat2. To use STAR, a genome directory specific for the STAR mapper needs to be generated first.  STAR tends to align more reads to pseudogenes compared to Tophat2.  However, the pseudogene problem can be significantly minimized by providing an annotation file containing known splice junctions. If no annotation is available for a genome of interest, a 2-pass mapping procedure is recommended. The first pass generates a splice junctions file, which is then used as the annotation file to run the second pass mapping.  
+STAR ([https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf manual]) is an ultrafast universal RNA-seq aligner.  It maps >60 times faster than Tophat2. To use STAR, a genome index specific for the STAR mapper needs to be generated first.  STAR tends to align more reads to pseudogenes compared to Tophat2.  However, the pseudogene problem can be significantly minimized by providing an annotation file containing known splice junctions. If no annotation is available for a genome of interest, a 2-pass mapping procedure is recommended. The first pass generates a splice junctions file, which is then used as the annotation file to run the second pass mapping.  
 
 Sample command: