User: nickhir

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nickhir10
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Status:
New User
Location:
german research cancer center (DKFZ)
Last seen:
1 week, 3 days ago
Joined:
4 months, 3 weeks ago
Email:
h*****************@gmail.com

Posts by nickhir

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Using StringTie with CAGE-seq data
... Could you elaborate what you mean? I only see two Cage signales, one in Intron 1 and around exon 2. Yet they predicted Isoforms with many more exons ...
written 28 days ago by nickhir10
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Using StringTie with CAGE-seq data
... Hi, I am currently reading a [paper][1] (Figure 3b) where they use CAGE-seq data as an input for StringTie, to assemble isoforms. I am very confused how this is possible, since I thought that only produces very short reads (~30bp) at the 5' end of our mRNA. I understand how StringTie works with RNA ...
stringtie written 28 days ago by nickhir10
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Merging BAM vs concatenate FASTQ
... Hi, i am fairly new to bioinformatics (genomics to be specific) so excuse me if this is a straight forward question. I have perforemd paired end WES which was performed across different lanes, so I have 2 fastq files per sample (4 in total). I know that I can merge BAM files after aligning each ...
genome sequencing written 4 weeks ago by nickhir10
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Comment: C: Questions about reference genome and alignment
... Thank you for linking that paper. But if I understood it correctly, the authers propose that the reference strand should be the watson strand. And the watson strand is the strand which has the 5' end at the short arm (p-arm). So isn't it correct if I am saying that the reference sequence starts at ...
written 5 weeks ago by nickhir10
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Comment: C: Questions about reference genome and alignment
... Thank you very much for your answer! This clears up a lot of things. > Genomes are reported as you pointed, from 5'->3' in the main chain, because there is a bias in the way genes are present in a > chromosome, genes prefer one chain over the other, so the '+' chain is the one with more g ...
written 5 weeks ago by nickhir10
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Questions about reference genome and alignment
... Hello everybody, I am fairly new to bioinformatics, so I have some basic concept questions that I hope you guys can help me to understand. I hope I'll manage to express myself properly, so you know what my questions are about. Let's say I download a reference genome, e.g. the new GRCh38. What I ...
genome assembly alignment written 5 weeks ago by nickhir10 • updated 5 weeks ago by JC11k
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How to download BAM file from VM
... Hey everybody, I am currently trying to download a BAM file, which is located on a VM to which I am connected over ssh (I want to look at the reads with IGV). Initially the download is reasonably fast (~7Mb/s), but after a while it goes down to (100kb/s) which means that the download takes over on ...
vm bam download written 11 weeks ago by nickhir10
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Find out genome version given fasta file
... Hello everybody, I just downloaded the primary assembly from the [GATK bundle][1] along with the dbsnp_146.vcf file (I need it for the BaseRecalibrator function). I assume, that the vcf file was created based on the primary assembly that I downloaded, given that they are in the same bundle, but I ...
genome assembly written 3 months ago by nickhir10
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Comment: C: Getting the db SNP VCF file for GRCh38.p13
... I have downloaded the latest version from that site, but that is VCF uses GRCh38.p2 instead of GRCh38.p13, which I require. ...
written 3 months ago by nickhir10
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Getting the db SNP VCF file for GRCh38.p13
... Hello everybody, after searching a long time, I am still unable to find the db SNP VCF file with the coordinatse for GRCh38.p13. The latest version of the db SNP VCF that I found was this [here][1]. However, after downloading it, I realized, that it uses GRCh38.p12. For context, I need the VCF ...
vcf dbsnp snp written 3 months ago by nickhir10 • updated 3 months ago by Nicolas Rosewick9.0k

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