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by katharina
Fri Nov 20, 2015 1:22 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by katharina on 18.12.2012 - 12:31
Can you please post your exact program call?
Katharina
by katharina
Fri Nov 20, 2015 1:22 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by -C on 15.12.2012 - 01:11
filterBam background jobs processing
When running filterBam the output is displayed in the terminal and once you run the job in the background you cannot disown it. Is there a command I can add to fix this?
by katharina
Fri Nov 20, 2015 1:22 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by katharina on 29.05.2012 - 10:24
The execution time for filterBam with --uniq and --paired flag took about 40 minutes for a 8.8 GB bam file on a Intel(R) Xeon(R) CPU 3.07GHz.
by katharina
Fri Nov 20, 2015 1:22 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by katharina on 29.05.2012 - 10:14 Tophat (or rather Bowtie) can directly produced "paired alignments". Our filterBam and bam2hints tools currently do not work with the paired bam format. Therefore, you'll need to run Tophat/Bowtie in 'single mode' and use the -1/-2 read pair name convent...
by katharina
Fri Nov 20, 2015 1:21 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by Cecilia on 24.05.2012 - 02:29 You're right. Tophat chopped off the /1 and /2 part so the read ID became something like 'HWIST945:92:d059facxx:5:1205:7877:128128'. How does 'samtools flagstat' tell whether the alignment is for read1 or read2? Since the stats show no duplicate, can I just obmit th...
by katharina
Fri Nov 20, 2015 1:21 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by katharina on 23.05.2012 - 22:57 Did you name the read pairs with a dash (-1, -2) instead of a slash (/1, /2) to indicate pairdness? Tophat/Bowtie cleave off the slash numbers, which means that filterBam will try for a veeeery long time to identify impossible pairs. This should eventually result ...
by katharina
Fri Nov 20, 2015 1:21 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

filterBam execution time

Originally posted in the old forum by Cecilia on 23.05.2012 - 21:52 I tried to run 'filterBam --uniq --paired --in input.bam --out filtered.bam'. The process has been running for more than 1 day and still not finished. The output file is empty. How long usually does filterBam take to run? The input...
by katharina
Fri Nov 20, 2015 1:21 pm
Forum: Predicting Genes with AUGUSTUS
Topic: bamtools filter
Replies: 3
Views: 3136

Re: bamtools filter

by Fred on 31.12.2012 - 00:07
Great. This is what I was looking for. Thanks!
by katharina
Fri Nov 20, 2015 1:20 pm
Forum: Predicting Genes with AUGUSTUS
Topic: bamtools filter
Replies: 3
Views: 3136

Re: bamtools filter

by katharina on 28.12.2012 - 17:55 This is an external script, but it has very simple contents: { "filters" : [ { "id" : "operation_N", "cigar" : "*N*" }, { "id" : "is_Mapped", "isMapped" : "true" } ], "r...
by katharina
Fri Nov 20, 2015 1:20 pm
Forum: Predicting Genes with AUGUSTUS
Topic: bamtools filter
Replies: 3
Views: 3136

Re: bamtools filter

by Fred on 21.12.2012 - 22:51
bamtools filter
Is the operation_N_filter.txt script in the bamtools toolkit or is this an external script.
by katharina
Fri Nov 20, 2015 1:20 pm
Forum: Predicting Genes with AUGUSTUS
Topic: bamtools filter
Replies: 3
Views: 3136

bamtools filter

Originally posted in the old forum by Fred on 21.12.2012 - 22:18 when trying to run bamtools filter -in output_directory/accepted_hits.bam -out output_directory/accepted_hits.noN.bam -script operation_N_filter.txt I receive the following error: bamtools filter ERROR: could not open script: operatio...
by katharina
Fri Nov 20, 2015 1:19 pm
Forum: WebAUGUSTUS
Topic: gff file for training, accepted features?
Replies: 1
Views: 2480

Re: gff file for training, accepted features?

by katharina on 16.01.2013 - 10:58 Hi Viola, the augustus web service will accept all features in your file, i.e. the upload of your file in its current format will be possible. However, the web service calls scripts of the AUGUSTUS distribution. The script gff2gbSmallDNA.pl that we use to convert ...
by katharina
Fri Nov 20, 2015 1:18 pm
Forum: WebAUGUSTUS
Topic: gff file for training, accepted features?
Replies: 1
Views: 2480

gff file for training, accepted features?

Originally posted in the old forum by Viola Manning on 15.01.2013 - 21:39 Hello Augustus folks, I would like to train Augustus to annotate multiple genomes of an organism that already is well annotated. To train Augustus, I see that I can use a gene structure file in gff format, which I have, but t...
by katharina
Fri Nov 20, 2015 1:18 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam and tophat2 question
Replies: 3
Views: 16055

Re: filterBam and tophat2 question

by katharina on 17.01.2013 - 12:09
Thanks, that would be great!
by katharina
Fri Nov 20, 2015 1:17 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam and tophat2 question
Replies: 3
Views: 16055

Re: filterBam and tophat2 question

by Jason on 17.01.2013 - 04:00
Thank you very much for your answer Katharina. I will email you our filters if we found anything useful
by katharina
Fri Nov 20, 2015 1:17 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam and tophat2 question
Replies: 3
Views: 16055

Re: filterBam and tophat2 question

by katharina on 14.01.2013 - 10:44 Hi Jason, you guessed correctly: our current protocol for using RNA-Seq as extrinsic evidence for AUGUSTUS supports only singleton mappings. We use our own filter to identify paired reads (filterBam). There are of course other possibilities if you already implemen...
by katharina
Fri Nov 20, 2015 1:17 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam and tophat2 question
Replies: 3
Views: 16055

filterBam and tophat2 question

Originally posted in the old forum by Jason on 14.01.2013 - 05:15 Hi, We have been using augustus for many of our species and have used custom scripts to retrieve intron hints from tophat2 bam files. I saw the augustus has new instructions on using rna-seq evidence (yes!) and would like to try it. ...
by katharina
Fri Nov 20, 2015 1:16 pm
Forum: Training AUGUSTUS
Topic: AutoAug.pl running with PASA+GMAP
Replies: 1
Views: 2218

Re: AutoAug.pl running with PASA+GMAP

by katharina on 21.01.2013 - 10:30
Hi Vickie,
thanks for telling us. I have included your comments in the README of autoAug.pl.
It might take a little while until it takes effect in the sources that are available for download since Mario has to make a new AUGUSTUS release.
Best,
Katharina
by katharina
Fri Nov 20, 2015 1:16 pm
Forum: Training AUGUSTUS
Topic: AutoAug.pl running with PASA+GMAP
Replies: 1
Views: 2218

AutoAug.pl running with PASA+GMAP

Originally posted in the old forum by Vickie on 18.01.2013 - 13:25 Hi, I'm writing this post because the AutoAug.pl README file is a little bit out of date. An exactly that part which advises to delete -S option from process_gmap_alignments.pl . Because of that, new PASA+GMAP starts complaining on ...
by katharina
Fri Nov 20, 2015 1:14 pm
Forum: Predicting Genes with AUGUSTUS
Topic: AUGUSTUS for transcriptome
Replies: 15
Views: 9109

Re: AUGUSTUS for transcriptome

by suzuki on 06.06.2013 - 13:06
I was wondering how I could provide you with examples?