User: jackfrost2199

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Washington D.C.
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theonejackfrost
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2 years, 7 months ago
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Posts by jackfrost2199

<prev • 16 results • page 1 of 2 • next >
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TCGA BRCA sample_type blood derived normal?
... I'm currently grabbing some BRCA data from TCGA. However I've noticed that the 'sample_type' field is 01 for primary solid tumor (as expected) but 10 for blood derived normal. I was expecting sample_type 11 for the normal tissue (solid tissue normal). Is normal breast tissue typically blood deriv ...
tcga written 3.3 years ago by jackfrost219970 • updated 7 months ago by bounlu190
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Comment: C: How to change Seqrecord id to numbers from a .txt file (Biopython)
... Great! I'm glad it worked for you especially since I don't use python much :D ...
written 3.3 years ago by jackfrost219970
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Answer: A: Gene Ontology mining from IDs
... If you're going to do a bunch of them in batch, probably downloading the GO ontology release (http://geneontology.org/page/download-ontology) and then extracting out the information you want through a small script would be the best way. If you have few enough you can do them by hand, I would say ju ...
written 3.3 years ago by jackfrost219970
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Answer: A: How to change Seqrecord id to numbers from a .txt file (Biopython)
... Try this: from Bio import SeqIO fout = open("output.fasta", "w") handle = open("input.fasta", "r") new_id=0 for seq_record in SeqIO.parse(handle, "fasta"): seq_record.id = new_id new_id =+ 1 seq_record.description = "" print seq_record. ...
written 3.3 years ago by jackfrost219970
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Comment: C: how to do further analysis after variant calling and annotation?
... No problem, I'm happy to help if you have any problems with the next steps. ...
written 3.3 years ago by jackfrost219970
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Comment: C: how to do further analysis after variant calling and annotation?
... If you want to visualize the VCFs you created, try IGV (http://www.broadinstitute.org/igv/). You've basically hit the end of the automatic pipeline where you can run one tool after another and have something meaningful without designing a bioinformatics experiment. Mutect2 did the equivalent of ...
written 3.3 years ago by jackfrost219970
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Answer: A: How to know the genome coordinate of DNaseI hypersensitive sites large peaks?
... Do you have the raw data or is the only data you have this bed file? Are these small regions adjacent to each other? It's possible that each small region has a certain signal, and multiple small regions together are showing the full broad peak (which could have a variety of different signal streng ...
written 3.3 years ago by jackfrost219970
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Answer: A: how to do further analysis after variant calling and annotation?
... I would suggest R. You can generate lots of different good visualizations there. It is free and pretty easy to use (although a little bit of a learning curve so hang in there). You just load the data you want and then tell it what to plot and how. You can do lots of customization and then fix is ...
written 3.3 years ago by jackfrost219970
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Comment: C: GTF format that's acceptable for Tophat/Cufflinks
... I see it in src/SeqAn-1.4.2/seqan/store/store_io_gff.h and src/tophat-fusion-post (although I think the second isn't relevant in this case). In the header file it looks like it is trying to match some type of key, which would make sense that it is looking in the info column of the GTF. I have to s ...
written 3.3 years ago by jackfrost219970
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Comment: C: VCF file REF column only contains N
... I think everything looks good. What is the size of "SC_Stressed.raw.bcf" after you do the mpileup stage but before the bcftools? ...
written 3.3 years ago by jackfrost219970

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