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Originally posted by rbagnall View PostI get the same error too.
Did you solve the problem Jason?
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Originally posted by PeteH View PostCheck that the reference annotation was successfully downloaded by NGSrich. In my case it was unable to download the annotation (due to firewall?) but once I manually downloaded the file and used the option -g <local_path_to_manually_downloaded_annotation> instead the program worked.
Nice tool but I would add to others comments that it would be good to enable .bam files too
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Originally posted by pfrommolt View PostDear All,
I would like to announce the inception of NGSrich, a software for evaluation of target enrichment performance in Illumina next-generation sequencing. An early release of the code has been uploaded to SourceForge at
but we're still working on a Java version. Regards,
Peter Frommolt
University of Cologne
I have run 5 Illumina samples with your program in and when I obtained the summary statistics I always obtain 2 reads more than the ones I obtain while doing a custom command in Linux. As I have written in my sam file "ILLUMINA" for every read, I do not understand why does NGSrich give me not the same number of reads.
grep -c ILLUMINA file
Example:
NGSrich: # Reads: 10754356
grep -c ILLUMINA myfile: 10754358
Can you help me? Thanks in advance
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Hey chariko,
Sometimes a sam header contains the PL:ILLUMINA (i.e. platform) in the read group.
If you show the first 10 lines of your grep'ed' output, is there an @RG.... line?
Originally posted by chariko View PostDear Peter,
I have run 5 Illumina samples with your program in and when I obtained the summary statistics I always obtain 2 reads more than the ones I obtain while doing a custom command in Linux. As I have written in my sam file "ILLUMINA" for every read, I do not understand why does NGSrich give me not the same number of reads.
grep -c ILLUMINA file
Example:
NGSrich: # Reads: 10754356
grep -c ILLUMINA myfile: 10754358
Can you help me? Thanks in advance
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Originally posted by rbagnall View PostHey chariko,
Sometimes a sam header contains the PL:ILLUMINA (i.e. platform) in the read group.
If you show the first 10 lines of your grep'ed' output, is there an @RG.... line?
Hi rbagnall,
First of all thank you for your answer but unfortunately I checked that and all the lines before the reads did not have any "ILLUMINA" written. As an example the first 30 lines of my file were:
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr1 LN:249250621
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chrM LN:16571
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@PG ID:bwa PN:bwa VN:0.5.9-r16
ILLUMINA-GA_0032:6:94:16...
Thanks
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Nice tool, some suggestions
1) Support for BAM files
2) Packaged program as a jar file
3) Ability to cap mapping quality
4) Ability to ignore reads flagged as duplicates (see SAM spec)
5) Consider a padding option for flanking N bases around a target region
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Dear, I have a problem in step1 with NGSrich:
I run by this command:
> java NGSrich -r sample.sam -a hg19 -t BED_SureSelect_exon.bed -T /tmp/
and the program returns me:
READS FILE:
sample.sam was reduced to /tmp/1309850911320sample_genoma1.5988.txt
Reduced file /tmp/1309850911320
sample_genoma1.5988.txt sorted
GENOME ANNOTATION FILE:
/tmp/1309850911320/refGene.genome reduced to /tmp/1309850911320/NGSrich_genome_genoma1.5988.txt
Exception in thread "main" java.lang.NumberFormatException: For input string: "chr1"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
at java.lang.Integer.parseInt(Integer.java:449)
at java.lang.Integer.parseInt(Integer.java:499)
at adapter.TargetAdapter.start(TargetAdapter.java:168)
at adapter.TargetAdapter.adapt(TargetAdapter.java:56)
at Enrichment.reduceFiles(Enrichment.java:185)
at NGSrich.main(NGSrich.java:91)
Could you help me?
Thanx a lot,
ME
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Bugs
1) I got two reads less than expected (as chariko did)
2) Mean coverage looks suspicious. At least in one sample where I expected about 50x coverage I got 501x coverage...
3) On target does not look correct for some samples (about double than expected)
Point 1 happens at every experiment, points 2 and 3 just sometimes...Last edited by scalabrin; 07-06-2011, 03:12 AM.
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Bug and bam supported in new version
Originally posted by scalabrin View Post1) I got two reads less than expected (as chariko)
2) Mean coverage looks suspicious. At least in one sample where I expected about 50x coverage I got 501x coverage...
3) On target does not look correct for some samples (double than expected)
>>> STEP 5: computing overall wiggle data
Start computing overall wiggle data
Align File Name: /tmp_path/1309882900147/NGSrich_filename_server.20189.txt
Output Dir: /output_path/data
Overall conversion in Wig unsuccessful
java.io.FileNotFoundException: /output_path/data/sapiens/share/NGSrich/mydata/tmp_enrichment.wig (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:209)
at java.io.FileOutputStream.<init>(FileOutputStream.java:160)
at java.io.FileWriter.<init>(FileWriter.java:90)
at converters.Read2Wig.convert(Read2Wig.java:89)
at converters.Read2Wig.<init>(Read2Wig.java:65)
at Enrichment.computeOverallWiggleFile(Enrichment.java:368)
at NGSrich.main(NGSrich.java:127)
Indeed 'sapiens' directory is not present in 'data'. Is there any problem in parsing paths? In my path (output_path) there is a homo_sapiens directory, perhaps you do not take into account underscores?
I tried both latests versions 0.4.3 and 0.4.4.
Last version does work (indeed it is a simple but effective work-around calling samtools to produce a temporary sam file!)
ps I had to cut path names as they represent private dataLast edited by scalabrin; 07-06-2011, 03:09 AM.
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2 missing reads
>>> STEP 1: reducing files
READS FILE:
/path/tmp/1309943569477/sample10.sam was reduced to /path/tmp/1309943569477/NGSrich_sample10_pinot.5066.txt
in the second file there is one line less, the last one. Perhaps you forgot to parse the last line (after a while loop?). And a similar error might contribute to the two missing reads!!!
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Hi,
My command :
[ngs@s-ngs-client-linux tools]$ java NGSrich -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -a /stockage/ngs-client-01/tools/samtools/test_target/ref/hg19_refGene.txt -t /stockage/ngs-client-01/tools/samtools/test_target/bed/baits_chr17_brca1.bed
Exception in thread "main" java.lang.NoClassDefFoundError: NGSrich
Caused by: java.lang.ClassNotFoundException: NGSrich
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:319)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:264)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332)
Could not find the main class: NGSrich. Program will exit.
????
Regards
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