User: archana.bioinfo87

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Posts by archana.bioinfo87

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Comment: C: In TCGA: R1 and R2 files are missing in fastq.gz
... Yes, thanks for this hint. I solved my problem. ...
written 5 weeks ago by archana.bioinfo87100
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Comment: C: In TCGA: R1 and R2 files are missing in fastq.gz
... I downloaded from this link https://portal.gdc.cancer.gov/legacy-archive/search/f As, I have access for controlled data sets. ...
written 6 weeks ago by archana.bioinfo87100
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In TCGA: R1 and R2 files are missing in fastq.gz
... Hi, I downloaded some RNA-seq data from TCGA. After doing untar I realized the R1 and R2 fastq files are not there. For example UNCID_2210756.2c113ebf-70de-4752-81de-a873f4f3db64.110324_UNC6-RDR300211_00088_FC_7090HAAXX_4.tar To untar this I used command "tar -xvf UNCI*.tar" And got a single fas ...
assembly next-gen rna-seq written 6 weeks ago by archana.bioinfo87100
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Comment: C: what next after DEGs?
... Its all depend on your work objectives because you can do "n" number of analysis in research. ...
written 7 weeks ago by archana.bioinfo87100
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Comment: C: sequence alignment of protein sequence
... Use standalone blast where you can make 1890 protein as a database (using makeblastdb) and rest 3 protein as a query. ...
written 7 weeks ago by archana.bioinfo87100
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Comment: C: BLAST multiple database against each other
... Dear, I think I already mentioned in my question that I have 9 different databases. Things which I already tried 1. I created 9 different databases using makeblastdb. And tried the loop for 1 database sequences blast with respect to other using loop. (~20 days ran but no result) 2. Tried the blast ...
written 7 weeks ago by archana.bioinfo87100
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Comment: C: BLAST multiple database against each other
... Sorry, may be I was unable to explain but I splited the query file not the DB. Already, I tried blastdb_aliastool but still waiting for result. I am sorting the BLAST result to get the exact matched sequences only. Thanks for your valuable suggestions. ...
written 8 weeks ago by archana.bioinfo87100
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Comment: C: BLAST multiple database against each other
... Thanks, yes i tested all databases before putting them in this big for loop. Till date only i can think the memory issue. Because for small seqeuences i am getting the results. Thanks all for your suggestions ...
written 8 weeks ago by archana.bioinfo87100
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Comment: C: BLAST multiple database against each other
... Thanks, but already i tested with small sequence before putting them in loop. ...
written 8 weeks ago by archana.bioinfo87100
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Comment: C: BLAST multiple database against each other
... Yes, only one database will match with another 8 one by one. ...
written 8 weeks ago by archana.bioinfo87100

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Popular Question 17 months ago, created a question with more than 1,000 views. For NCBI error report

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