Description:
This is the user's forum for GNUMAP. Questions and comments posted here will be watched by the authors who will be quick to respond. Notices of errors or bugs are also helpful.
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Paired end
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Hi-
Does GNUMAP align paired end data (as opposed to only aligning them as
single end reads)?
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reads that align to multiple places
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Dear all, please could you suggest an appropriate combination of parameters I can use in order to output : <> the reads that align uniquely <> the reads that align to less than 10, or less than 100, 1000 places <> if a read aligns to multiple places, one random place can be chosen thanks a lot, Bogdan... more »
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ld: unknown option: -Bstatic
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Hi,
When i do make to install Gnumap, i have this error :
ld: unknown option: -Bstatic
collect2: ld returned 1 exit status
make: *** [bin/gnumap] Error 1
I have got a solution please ?
Thanks
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Converting FASTQ quality scores
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Hello-
Is there a way to tell GNUMAP not to convert FASTQ quality scores?
We are using data from Illumina 1.5+ pipeline, quality scores are
Phred (3,40) using ASCII 66-104. We convert the qseq.txt files to
Sanger-encoded FASTQ files for use in GNUMAP and other aligners.
We run the alignments through a few other QC steps (deduping, local... more »
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GNUMAP Version 2.6.0
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GNUMAP users, The latest version of GNUMAP (version 2.6.0) has just bee uploaded to the website. You can download by going here: [link], or straight to the link at [link]. Most important, this release made significant improvements to bisulfite mapping to include BSW, BSWR, BSC, and BSCR reads (for a full description of these sequence types and flags for mapping them, please see [link]).... more »
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'std::bad_alloc'
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Hello, I am now using your software but I get the foollowing:
fatallis@fatallis-G60J:~/gnuma p/bin$ ./gnumap-plain -g '/home/fatallis/
Escritorio/ZmB73_RefGen_v2/chr 1.fasta' -o EIChr1 -a .9 -p -v 1 -c 8 -T
1000000 -M 0 --print_all_sam '/home/fatallis/Escritorio/
ZmB73_RefGen_v2/IE-16-30-W3.fa sta'... more »
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GNUMAP Defaults
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Nathan, Can you make -p -a .9 default parameter settings for GNUMAP? To my knowledge, everyone is using -p and most are using something similar to -a .9 Thanks! Evan
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RNA editing with GNUMAP
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Brent, Are you sure it is not working? Are you accounting for the fact that GNUMAP reports the positive strand bases, and therefore you are looking for T->C changes when you are looking for negative strand editing? I guess this depends on whether you are using .sgrex or .sam for your analysis. If this is not the problem, then Nathan can you address this issue ASAP? I think this is the same problem we are having with our bisulfite mapping.... more »
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