Not currently... I can add that, though. I'll make a note to do that. BBMap has an "idfilter" flag, though.
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I just uploaded a new version of BBTools - 36.11 - that supports idfilter (and subfilter, editfilter, etc) in Reformat. Bear in mind that reads mapped using old-style cigar strings ('M' symbol instead of 'X' and '=') must also have MD tags. For newer cigar strings MD tags are not necessary. Unmapped reads will not be affected by this filter (they will pass the filter), so if you want to get rid of them you also need to set "mappedonly=t".
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I am not sure this is a bug or not, but when I try to use reformat.sh (version 37.76) to add fake qualities of Q30 to a PacBio Sequel fastq file (produced withCode:bamtools convert -format fastq -in sequel.subreads.bam -out sequel.subreads.fastq
Code:/opt/bbmap/reformat.sh qin=33 qout=33 qfake=30 in=sequel.subreads.fastq out=sequel.subreads.fqual.fastq
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Hi,
Can I use reformat or any other bbtools script to split my fasta file into sub-files?
eg X.fa (100 sequences) -> X01.fa X02.fa....X10.fa (each with 10 sequences)?
I don't mind whether I need to select the number of sequences per file or total number of files and it doesn't really matter what order the sequences are in as long as there is no duplication of sequences.
Cheers,
Dave
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Hi Brian Bushnell,
when I used mapPacBio.sh for mapping pacbio reads. I met the errors as following:
Exception in thread "Thread-23" java.lang.AssertionError: Read 20, length 10550, exceeds the limit of 6019
You can map the reads in chunks by reformatting to fasta, then mapping with the setting 'fastareadlen=6019'
at align2.AbstractMapThread.run(AbstractMapThread.java:480)
But I did not find how I can reformat it.
Could you help me figure out this issue?
Thanks,
Fuyou
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Originally posted by GenoMax View PostYou can useCode:reformat.sh in=your_file.fastq out=newfile.fa
That said I think mapPacBio.sh should automatically split reads longer than 6k when it does mapping. Is that not working?
Thanks,
Fuyou
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hello folks, I am trying to work on a FASTQ file using reformat.sh, although I have correctly installed Java and tested it in the command line, I still can't get it to work. It seems the problem is that I don't have the FASTQ file in the same directory as the BBMap folder, could that be an issue?
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pepe84, do you provide a path to the file? Please copy your command as tried, and then copy the error message.Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com
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here is the command:
java -cp C:\BBMap\current\jgi.ReformatReads in=“C:\BBMap\resources\SRRXXXXX.fastq” out1=EFB_R1.fq out2=EFB_R2.fq
And here is the error:
Error: Could not find or load main class in=C:\BBMap\resources\SRRXXXXX.fastq
Just an FYI I am using the command line on windows.
Thanks, I appreciate any help
Originally posted by SNPsaurus View Postpepe84, do you provide a path to the file? Please copy your command as tried, and then copy the error message.
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reformat.sh hangs in sleep status
I used demuxbyname.sh to split four lanes of Illumina data into separate files for 84 samples, and now I'm running a loop with reformat.sh to rename the samples from the index sequences to more biologically relevant names, catenate all four lanes of data from the same sample together, and produce a single file of gzipped interleaved output. The loop is running on a cluster with 37.41 installed, and worked fine for the first 51 samples of the 84, but hung on sample 52. ACode:ps aux | grep <user>
Code:<user> 14126 0.6 0.0 6610600 250716 ? Sl 00:21 4:42 java -ea -Xmx200m -cp /isg/shared/apps/bbmap/37.41/current/ jgi.ReformatReads in=L6_GAGATTCC+CTTCGCCT_#.fq out=L6_A2.fq
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