User: a.james
a.james • 210
- Reputation:
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- Germany
- Last seen:
- 2 months ago
- Joined:
- 5 years, 2 months ago
- Email:
- a******@dkfz-heidelberg.de
Posts by a.james
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... Thank you I need the following information in the metadata file,
study tcga_id analysis_id refassembly mark_duplicates exome_bed
However, I I can have them also in from BAM header, but was looking for a programmatic way, way. ...
written 10 weeks ago by
a.james • 210
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... Ok, I see so such informatiin should be generated directly from the BAM file. Ok thanks.I thought I will have them seperetely as metedata. Ok Thanks for clarification ...
written 10 weeks ago by
a.james • 210
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... Thank you. I have downloaded the tsv files from clinical information from the portal directly. however, I have no information for columns, say for example, `mark_duplicates refassembly` etc.
...
written 10 weeks ago by
a.james • 210
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... Ok, I have 320 AML aligned exon files (BAM or `*_gdc_realn.bam` ) files, in addition to that, I have their manifest data with `UUID, filename, md5, size, adn state`. I would to have their metadat as `tsv` file. Currently, all I have is these BAM files and there manifest data. All I need is, the me ...
written 10 weeks ago by
a.james • 210
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... @kelvin, Thanks for the reply. I have 350 samples. And I would like to have a more efficient method for all samples than manually downloading the metadata file. Also is there a way to have the metadata file in `tsv` fomart given the manifest data with the UUID's ...
written 10 weeks ago by
a.james • 210
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... @david.peeney, How and where did you download the metadata.cart* from GDC? ...
written 10 weeks ago by
a.james • 210
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... Hello All,
I have exon datasets (aligned BAM) files downloaded. I now need the metadata information for the same samples. How can I download or extract them given the manifest information of all samples.
I have read through the [GDC API][1], however, I am not clear how could get the metadata as t ...
written 10 weeks ago by
a.james • 210
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... The README looks like this
GRCh37-lite-+-HPV_Redux-build consists of GRCh37-lite appended with a nonredundant subset of common human papilloma viruses. Included are HPV types 1 (NC_001356.1), 2 (NC_001352.1), 4 (NC_001457.1), 5 (NC_001531.1), 6 (NC_001355.1), 7 (NC_001595.1), 9 (NC_001596.1), ...
written 12 weeks ago by
a.james • 210
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... Thank you for the description. I will try with this file. @genomax, May I know where could I get the viral sequences ...
written 12 weeks ago by
a.james • 210
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... `grep -c "^>" GRCh37-lite.fa`
84
`grep -c "^>" all_sequence.fa`
123
`grep "^>" GRCh37-lite.fa | tail -10`
>GL000224.1 Homo sapiens unplaced genomic contig, GRCh37 reference primary assembly
>GL000223.1 Homo sapiens unplaced genomic contig, GRCh37 reference primary assembl ...
written 12 weeks ago by
a.james • 210
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