Forum: Bioinformatics
08-12-2020, 12:51 PM
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Replies: 57
Views: 60,671
Hi all,
does any one has experience with...
Hi all,
does any one has experience with processing ancient DNA using bbtools? My question is how short the kmer length for bbnorm should be, regarding issues with the fragmented DNA. Thanks in...
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Forum: Bioinformatics
04-17-2020, 03:32 AM
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Replies: 0
Views: 1,180
in silico PCR benchmarking
Dear community,
I wonder whether anybody ever did a benchmarking of in silico PCR tools? I couldn't find any benchmarking so far.
Are there any tools you could recommend for command line usage...
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Forum: Bioinformatics
01-05-2020, 02:27 AM
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Replies: 34
Views: 24,391
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Forum: Bioinformatics
01-05-2020, 02:10 AM
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Replies: 34
Views: 24,391
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Forum: Metagenomics
09-10-2019, 04:17 AM
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Replies: 4
Views: 9,669
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Forum: Metagenomics
09-09-2019, 03:50 AM
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Replies: 4
Views: 9,669
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Forum: Metagenomics
09-03-2019, 02:21 AM
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Replies: 0
Views: 5,235
Taxonomy tree conflicts in Greengenes V 13.5
Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database...
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Forum: Metagenomics
09-03-2019, 01:52 AM
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Replies: 4
Views: 9,669
Taxonomy tree conflicts in Greengenes V 13.5
Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database...
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Forum: Bioinformatics
03-07-2019, 03:19 AM
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Replies: 252
Views: 118,045
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Forum: Bioinformatics
06-01-2018, 02:19 AM
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Replies: 132
Views: 88,560
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Forum: Bioinformatics
03-21-2018, 05:12 AM
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Replies: 1
Views: 2,386
Update
Okay, I gave up on bioperl and wrapped my tabular output.
I got a multidimensional hash structure now.
How may I compare all qstart/qend values of %result{$consensus} and keep only the once which...
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Forum: Bioinformatics
03-16-2018, 08:01 AM
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Replies: 1
Views: 2,386
Parsing Blast xml using Perl (BioPerl)
Hi people,
I'd like to resolve the following problem(s):
I'm trying to resolve the structure of reads, partial of retroviral origin, partial of host genomic origin. In addition, I'd like to...
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Forum: Bioinformatics
01-09-2018, 11:24 AM
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Replies: 0
Views: 2,010
Haplotype network indels HELP!
Hi all,
I'd like to create a haplotype network including 8 different groups. I have 326 sequences and 84 haplotypes. Some of the haplotypes only differ in indels, but they are real!
I tried R pegas...
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Forum: Bioinformatics
07-27-2017, 02:18 AM
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Replies: 2
Views: 1,918
Okay, I now might know why bcftools fails (to...
Okay, I now might know why bcftools fails (to many real gaps in long reads which might be sorted out then). Any other suggestions? I do not find an up to date best practice for GATK3/4 or did anyone...
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Forum: Bioinformatics
07-23-2017, 04:35 AM
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Replies: 2
Views: 1,918
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Forum: Bioinformatics
07-20-2017, 03:17 AM
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Replies: 2
Views: 1,918
Consensus Calling BCFTOOLS PacBio gaps
Dear community,
I mapped reads from targeted sequencing (PacBio ccs) to a reference (BMA mem - local alignment because I got inverse PCR reads). Most often the complete reference is not covered. I'd...
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Forum: Bioinformatics
11-23-2016, 01:03 PM
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Replies: 3
Views: 4,086
Hi Brian,
Thanks for your reply! I forgot to...
Hi Brian,
Thanks for your reply! I forgot to mention, I want to keep the reads untrimmed. And would your software care about the "both primers present" issue? Otherwise I have again to check every...
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Forum: Bioinformatics
11-23-2016, 06:17 AM
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Replies: 3
Views: 4,086
Demultiplexing PacBio sequences
Hi all,
I have the following problem:
I have a dataset containing circurlarized and linear DNA. It was amplified with two pairs of primers using inverse PCR. I'd like to dissect the data by the...
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Forum: Bioinformatics
11-20-2015, 03:31 AM
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Replies: 13
Views: 2,223
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Forum: Bioinformatics
11-20-2015, 03:13 AM
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Replies: 13
Views: 2,223
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Forum: Bioinformatics
11-20-2015, 01:43 AM
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Replies: 13
Views: 2,223
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Forum: Bioinformatics
11-19-2015, 09:43 AM
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Replies: 13
Views: 2,223
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Forum: Bioinformatics
11-19-2015, 09:13 AM
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Replies: 13
Views: 2,223
@ Brian,
they are self-corrected and no, no...
@ Brian,
they are self-corrected and no, no metagenomics, no 16S reads -> inverse PCR reads one organism.
@ GenoMax,
clustal had no problems with the long names. I'm done with everything, the...
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Forum: Bioinformatics
11-19-2015, 07:49 AM
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Replies: 13
Views: 2,223
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Forum: Bioinformatics
11-19-2015, 06:18 AM
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Replies: 13
Views: 2,223
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