User: Benedek Dankó

Reputation:
10
Status:
New User
Location:
Budapest, Hungary
Website:
https://www.linkedin.c...
Last seen:
1 month, 1 week ago
Joined:
10 months, 4 weeks ago
Email:
d***********@gmail.com

I am a bioinformatics MSc. student at Eötvös Lóránd University in Budapest, Hungary.

As a student researcher, I work at the Bioinformatics Group of the 1st Department of Pathology and Experimental Cancer Research of Semmelweis University.

Posts by Benedek Dankó

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Which transcriptome assembler is recommended for short-read cancer transcriptome
... Around 30 million (paired-end) per sample but there are samples with more (eg. 60-70 million). ...
written 11 weeks ago by Benedek Dankó10
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Which transcriptome assembler is recommended for short-read cancer transcriptome data?
... Hello! I would like to do a de-novo transcriptome assembly on human control/cancer, short-read RNA-seq datasets. I would like to identify possible unannotated (cancer-specific) transcripts. Which assembler software would you recommend to use in this case? Our server has 24 cores, 94 Gb RAM, so any ...
assembly short-read rna-seq cancer written 11 weeks ago by Benedek Dankó10
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Answer: A: can picard use multiple threads?
... You can use for example GNU parallel. Something like this: ls *.bam | sed 's/.bam.*//' | parallel --eta -j "java -jar picard I={}.bam O={}_out.bam" ...
written 12 weeks ago by Benedek Dankó10
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Comment: C: STAR genomeLoad issue
... Hello, if I follow your instructions I get this error: ``` Jun 22 20:41:50 ...... FATAL ERROR, exiting ./STAR_alignment_paired_2.sh: line 17: --genomeLoad: command not found ``` The 17th line of my code is inside the for loop which would iterate over the read pairs. So maybe the --genomeLoad comm ...
written 5 months ago by Benedek Dankó10
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Comment: C: Checking integrity of SRA downloaded fastq files
... As far as I know, you can validate files with .sra extension, which are temporary files created by fastq-dump while downloading data from SRA. ...
written 5 months ago by Benedek Dankó10
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Comment: C: calling BWA mem from within python
... Thanks, this worked for me (Python 3.7). It seems that BWA doesn't work properly with os.subprocess(), but instead os.system() works perfectly. The bug about os.subprocess() should be something with output handling, I'm not sure. ...
written 10 months ago by Benedek Dankó10

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