Recent changes to CLASS

CLASS modified by mourisl

mourisl — Wed, 17 May 2017 19:43:16 -0000

--- v51
+++ v52
@@ -116,7 +116,8 @@
     Handle non-canonical splice sites.
     Fix a bug for the untraditional chromosomes (i.e. chr14_GL000009v2_random,...)
     Automatically decide whether to ignore reads with different read length by default.
-
+ * 5/17/2017 CLASS v2.1.7
+    Fix more bugs that resulting in no report of transcripts after some chromosomes.

 ### Terms of use ###

CLASS modified by mourisl

mourisl — Wed, 08 Feb 2017 17:05:33 -0000

--- v50
+++ v51
@@ -55,8 +55,16 @@

 ### Input/Output ###

-The primary input to CLASS is a set of short read alignments in BAM format and sorted by chromosome and position, for instance one produced with the program Tophat2 (http://tophat.cbcb.umd.edu).
-  
+The primary input to CLASS is a set of short read alignments in BAM format and sorted by chromosome and position, for instance one produced with the program [[Tophat2](http://tophat.cbcb.umd.edu)].
+
+CLASS requires XS field in BAM file to know the strand of spliced alignment. If the tools does not provide XS field, such as the default behavior of [[STAR](https://github.com/alexdobin/STAR)], you can use the program "addXS" in the package to add XS field to the BAM file. You can run "addXS" as:
+
+* ./addXS reference_genome.fa < sam_file
+
+The typical usage with BAM file can be:
+
+* samtools view -h in.bam | ./addXS reference_genome.fa | samtools view -bS - > out.bam 
+
 Given an alignment input x.bam, CLASS produces two intermediate data files, x.depth and x.splice in the temporary working directory..

   * The format of the x.depth file, generated by samtools, is:

CLASS modified by mourisl

mourisl — Wed, 08 Feb 2017 17:02:35 -0000

--- v49
+++ v50
@@ -103,6 +103,13 @@
    Ignore reads with different read length by default.
    Identify more alternative 3',5'-UTR.
    Fix a bug when read depth is 0 on a position.      
+ * 2/8/2017 CLASS v2.1.6:
+    Add XS field if the aligner does not provide such information in BAM file.
+    Handle non-canonical splice sites.
+    Fix a bug for the untraditional chromosomes (i.e. chr14_GL000009v2_random,...)
+    Automatically decide whether to ignore reads with different read length by default.
+
+

 ### Terms of use ###

CLASS modified by Liliana Florea

Liliana Florea — Sat, 15 Oct 2016 01:02:41 -0000

--- v48
+++ v49
@@ -43,11 +43,11 @@
       \-\-clean: whether to remove the temporary files in -wd (default: no)

 Alternatively, run the programs in succession, for instance:
-     mkdir sample.d; cd sample.d
-     ln -s $BAMFILEPATH/accepted_hits.bam sample.bam
-     samtools depth sample.bam > sample.depth
-     junc sample.bam -a > sample.splice
-     class ./sample -l sample -p 8 > sample.class.gtf
+         mkdir sample.d; cd sample.d
+         ln -s $BAMFILEPATH/accepted_hits.bam sample.bam
+         samtools depth sample.bam > sample.depth
+         junc sample.bam -a > sample.splice
+         class ./sample -l sample -p 8 > sample.class.gtf
 where $BAMFILEPATH is the path to the BAM file and 'sample' is the prefix associated with the run.

CLASS modified by Liliana Florea

Liliana Florea — Sat, 15 Oct 2016 01:01:29 -0000

--- v47
+++ v48
@@ -43,13 +43,11 @@
       \-\-clean: whether to remove the temporary files in -wd (default: no)

 Alternatively, run the programs in succession, for instance:
-
-    mkdir sample.d; cd sample.d
-    ln -s $BAMFILEPATH/accepted_hits.bam sample.bam
-    samtools depth sample.bam > sample.depth
-    junc sample.bam -a > sample.splice
-    class ./sample -l sample -p 8 > sample.class.gtf
-
+     mkdir sample.d; cd sample.d
+     ln -s $BAMFILEPATH/accepted_hits.bam sample.bam
+     samtools depth sample.bam > sample.depth
+     junc sample.bam -a > sample.splice
+     class ./sample -l sample -p 8 > sample.class.gtf
 where $BAMFILEPATH is the path to the BAM file and 'sample' is the prefix associated with the run.

CLASS modified by Liliana Florea

Liliana Florea — Sat, 15 Oct 2016 00:59:37 -0000

--- v46
+++ v47
@@ -41,6 +41,17 @@
       \-\-verbose: also output the procedure of CLASS (default: no)
       \-\-wd temporary_file_directory: the directory storing the temporary files (default: ./class_tmp)
       \-\-clean: whether to remove the temporary files in -wd (default: no) 
+
+Alternatively, run the programs in succession, for instance:
+
+    mkdir sample.d; cd sample.d
+    ln -s $BAMFILEPATH/accepted_hits.bam sample.bam
+    samtools depth sample.bam > sample.depth
+    junc sample.bam -a > sample.splice
+    class ./sample -l sample -p 8 > sample.class.gtf
+
+where $BAMFILEPATH is the path to the BAM file and 'sample' is the prefix associated with the run.
+

 *IMPORTANT*: Using external gene evidence generally improved the results when used within the 'set-cover' version. You can find an 'evidence' file, consisting of spliced alignments of human EST and RefSeq mRNA sequences, [[here](https://sourceforge.net/projects/splicebox/files/)]. Alignments were produced with the software [[ESTmapper/sim4db](http://sourceforge.net/projects/kmer)]. When using external gene evidence, it is recommended to use the -a argument when running junc.

CLASS modified by mourisl

mourisl — Tue, 09 Aug 2016 19:53:45 -0000

--- v45
+++ v46
@@ -3,7 +3,7 @@
 Described in:

 Current (dynamic-programming) version:
-Song, L., Sabunciyan, S., and Florea, L. (2016). CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.* Nucleic Acids Research 2016;* doi: 10.1093/nar/gkw158 . [[Free full text](http://nar.oxfordjournals.org/content/early/2016/03/13/nar.gkw158.abstract)]
+Song, L., Sabunciyan, S., and Florea, L. (2016). CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.* Nucleic Acids Res. 2016 Jun 2;44(10):e98.* doi: 10.1093/nar/gkw158 . [[Free full text](http://nar.oxfordjournals.org/content/44/10/e98.abstract)]

 Previous ('set cover') version:
 Song, L. and Florea, L. (2013). CLASS: Constrained Transcript Assembly of RNA-seq Reads.

CLASS modified by mourisl

mourisl — Fri, 29 Jul 2016 18:44:38 -0000

--- v44
+++ v45
@@ -36,6 +36,7 @@
       \-l label: add a prefix and a "_" to the ids in the GTF file (default: not used)
       \-j junction: the path to the splice junction file
       \-e evidence: the path to the evidence files
+      \-\-var_rd_len: extensive variable read lengths, i.e. reads after trimming (default: no)
       \-\-set-cover: use set cover to build transcripts from splicing graph (default: no)
       \-\-verbose: also output the procedure of CLASS (default: no)
       \-\-wd temporary_file_directory: the directory storing the temporary files (default: ./class_tmp)
@@ -89,8 +90,10 @@
 * 1/28/2016 CLASS v2.1.3:
      Introduce the "-l" option to add a prefix to the ids in the GTF file
      Add the version and command line information to the output  
-* 3/17/2016 CLASS v2.1.4:
-     Improve the accuracy when giving the annotation through -e option        
+* 7/29/2016 CLASS v2.1.5:
+   Ignore reads with different read length by default.
+   Identify more alternative 3',5'-UTR.
+   Fix a bug when read depth is 0 on a position.

 ### Terms of use ###

CLASS modified by Liliana Florea

Liliana Florea — Sun, 10 Apr 2016 00:58:27 -0000

--- v43
+++ v44
@@ -9,7 +9,7 @@
 Song, L. and Florea, L. (2013). CLASS: Constrained Transcript Assembly of RNA-seq Reads. 
 *Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing - RECOMB-SEQ 2013*. *BMC Bioinformatics* 14(Suppl. 5), S14. [[Free full text](http://www.biomedcentral.com/1471-2105/14/S5/S14/)]

-Copyright (C) 2012-2013, and GNU GPL, by Li Song, Liliana Florea
+Copyright (C) 2012-2016, and GNU GPL, by Li Song, Liliana Florea

 Includes portions copyright from:

CLASS modified by Liliana Florea

Liliana Florea — Sun, 10 Apr 2016 00:57:51 -0000

--- v42
+++ v43
@@ -29,7 +29,7 @@

 Usage: perl run_class.pl \[options\]
 Options:
-      \-a alignment_file (REQUIRED): the path to the alignemtn file(in BAM format)
+      \-a alignment_file (REQUIRED): the path to the alignment file(in BAM format)
       \-o output_file: the file storing the output of CLASS (default: ./alignment_file_wo_extension.gtf)
       \-p number_of_threads: specify the number of worker threads (default:1)
       \-F f: do not report the transcripts whose abundance level is lower than f*|most expressed transcript| in a gene
@@ -38,10 +38,10 @@
       \-e evidence: the path to the evidence files
       \-\-set-cover: use set cover to build transcripts from splicing graph (default: no)
       \-\-verbose: also output the procedure of CLASS (default: no)
-      \-\-wd tempoaray_file_directory: the directory storing the temporary files (default: ./class_tmp)
-      \-\-clean: whehter to remove the temporary files in -wd (default: no) 
+      \-\-wd temporary_file_directory: the directory storing the temporary files (default: ./class_tmp)
+      \-\-clean: whether to remove the temporary files in -wd (default: no) 

-*IMPORTANT*: Using external gene evidence generally improved results with the 'set-cover' version. You can find an 'evidence' file, consisting of spliced alignments of human EST and RefSeq mRNA sequences, [[here](https://sourceforge.net/projects/splicebox/files/)]. Alignments were produced with the software [[ESTmapper/sim4db](http://sourceforge.net/projects/kmer)]. When using external gene evidence, it is recommended to use the -a argument when running junc.
+*IMPORTANT*: Using external gene evidence generally improved the results when used within the 'set-cover' version. You can find an 'evidence' file, consisting of spliced alignments of human EST and RefSeq mRNA sequences, [[here](https://sourceforge.net/projects/splicebox/files/)]. Alignments were produced with the software [[ESTmapper/sim4db](http://sourceforge.net/projects/kmer)]. When using external gene evidence, it is recommended to use the -a argument when running junc.

 ### Input/Output ###

@@ -57,7 +57,7 @@

     *NOTE*: When using the '-a' argument in junc, the value #_of_supporting_reads can be negative, indicating that this splice junction is invalid.

-Lastly, to produce a set of transcripts, the program 'class' takes as input a BAM/SAM file, the depth file generated by 'samtools' and the splice junction file generated by 'junc'. The final output, consisting of predicted transcripts, is in standard GTF format.
+Lastly, to produce a set of transcripts, the program 'class' takes as input a BAM/SAM file, the depth file generated by 'samtools' and the splice junctions file generated by 'junc'. The final output, consisting of predicted transcripts, is in standard GTF format.

 *NOTE*: 'samtools' can only read a BAM file, while 'junc' and 'class' can read both SAM and BAM formats.

@@ -76,21 +76,21 @@
    Use static linked library of lpsolve55.
    Improve the precision of intron retention.
 * 5/9/2014 CLASS v2.0.0:
-   Improved sensitivity of transcriptome assembly
-   Supporting multi-threads
+   Improve the sensitivity of transcriptome assembly
+   Support multi-threads
 * 2/9/2015 CLASS v2.1.0:
-   Use a new wrapper to run CLASS. 
-   Change the transcript_id field in the GTF file as "chr_id.gene_id.txpt_id".
-   Add samtools package into release.
+   Use a new wrapper to run CLASS 
+   Change the transcript_id field in the GTF file to "chr_id.gene_id.txpt_id".
+   Add samtools package into the release
 * 5/19/2015 CLASS v2.1.1:
    Fix a bug in the wrapper
 * 10/21/2015 CLASS v2.1.2:
-   Fix a serious bug introduced from v2.0.0 which breaks the predicted transcripts into fragments.
+   Fix a serious bug introduced in v2.0.0 which breaks the predicted transcripts into fragments
 * 1/28/2016 CLASS v2.1.3:
-     Introduce "-l" option to add a prefix to the ids in the GTF file.
-     Add the version and command line information to the output.  
+     Introduce the "-l" option to add a prefix to the ids in the GTF file
+     Add the version and command line information to the output  
 * 3/17/2016 CLASS v2.1.4:
-     Improve the accuracy when giving annoation through -e option.        
+     Improve the accuracy when giving the annotation through -e option        

 ### Terms of use ###