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I'm trying to add kraken to my analysis pipelines and am getting a the following issue in my output:
[2018-08-02T21:34Z] System YAML configuration: /usr/local/share/bcbio/galaxy/bcbio_system.yaml
…
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### Bug description
https://www.hardwoodgenomics.org/organism/Juglans/regia?tripal_pane=group_reference_genome
not a bug necessarily, but certainly a casuality of #345
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Relies on this issue: https://github.com/AlexsLemonade/refinebio/issues/163
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In the GRCh38 transcriptome you can get from Ensembl, there is at least one gene that is identical except for the fact that it appears both on the primary assembly and in an alternative locus. Ensembl…
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We need to report statistics for the content of our database:
>Hi Jill and Meg,
>
>Is it possible for you to provide numbers for the data types in your databases such as we are reporting for GDR …
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Hi Brian,
As I mentioned during our meeting ~2 weeks ago, we have an issue that Trinity does not assemble full-length genes that should be present in the transcriptome, because we already cloned th…
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Hi,
This is a suggestion rather than an issue. I like how Trinity allows supplying multiple sequencing datasets via the --samples_file parameter. My suggestion is that this samples file should also c…
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Dear Dr. Brian,
I try to mapping my paired read with reference genome using align_and_estimate_abundance.pl in trinity program. TRANSCRIPT is the **V_corymbosum_scaffold_May_2013.fasta**
However, …
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hi
i ran mixcr with and without -p kaligner2 and got:
WITH:
Analysis Date: Mon Dec 17 10:38:55 GMT 2018
Input file(s): IB-031218-1_S1_L001_R1_001.TRIM.fastq.gz,IB-031218-1_S1_L001_R2_001.fastq.gz
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ibseq updated
5 years ago
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Dear , When I ran Hisat2 (version: 2.1.0) with --dta ( --downstream-transcriptome-assembly OR --dta-cufflinks), there was no XS tag in output file. I did not know how to fix it.
Thank you very much!