User: a.james

gravatar for a.james
a.james210
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210
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Location:
Germany
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2 months ago
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5 years, 2 months ago
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a******@dkfz-heidelberg.de

Posts by a.james

<prev • 90 results • page 1 of 9 • next >
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Comment: C: How to retrieve metadata from the manifest data and UUID from genomic data commo
... 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.james210
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... 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.james210
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... 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.james210
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... 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.james210
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... @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.james210
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... @david.peeney, How and where did you download the metadata.cart* from GDC? ...
written 10 weeks ago by a.james210
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How to retrieve metadata from the manifest data and UUID from genomic data commons (GDC)
... 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 ...
tcga next-gen alignment mutations exon written 10 weeks ago by a.james210
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Comment: C: Where can I download GRCh38-lite.fa file and all_sequences.fa file for hg38 vers
... 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.james210
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Comment: C: Where can I download GRCh38-lite.fa file and all_sequences.fa file for hg38 vers
... 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.james210
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Comment: C: Where can I download GRCh38-lite.fa file and all_sequences.fa file for hg38 vers
... `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.james210

Latest awards to a.james

Scholar 4 months ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 4 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 6 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 7 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 18 months ago, created a question with more than 1,000 views. For GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 18 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 18 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 21 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 2.2 years ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to find the frame shift information from fusion gene sequence
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq output from RNA-seq
Popular Question 2.8 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Student 3.1 years ago, asked a question with at least 3 up-votes. For ALL RNA-seq publicly available data
Popular Question 3.1 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 3.2 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Scholar 3.2 years ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Supporter 3.2 years ago, voted at least 25 times.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Pathway Graphs for gene set from RNA-seq
Popular Question 3.7 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 3.8 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data

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