User: Niek De Klein

gravatar for Niek De Klein
Niek De Klein2.4k
Reputation:
2,410
Status:
Trusted
Location:
Netherlands
Website:
http://-
Last seen:
20 hours ago
Joined:
8 years ago
Email:
n**********@gmail.com

4th year bioinformatics student

Posts by Niek De Klein

<prev • 248 results • page 1 of 25 • next >
0
votes
1
answer
190
views
1
answers
Comment: C: How to convert fastq to cram, and from cram back to fastq
... I made a stupid mistake, was counting lines of the gzipped fastq file and comparing to an unzipped fastq file. After fixing that there was still a small difference, as STAR by default doesn't put unmapped reads in the output file, so had to --outSAMunmapped Within option. After that I got the corr ...
written 15 days ago by Niek De Klein2.4k
0
votes
1
answer
190
views
1
answers
Comment: C: How to convert fastq to cram, and from cram back to fastq
... Thanks, I'm testing this now and seeing how it compares to removing secondary aligned reads ...
written 22 days ago by Niek De Klein2.4k
2
votes
1
answer
190
views
1
answer
How to convert fastq to cram, and from cram back to fastq
... I want to save my fastq files as CRAM files to save space. However, I do want to be able to get the reads back that I have in my fastq, in case I have to reallign in a different way in the future. Below I have the code that I use to do the conversions to BAM and back again. However, when I then chec ...
fastq cram written 23 days ago by Niek De Klein2.4k • updated 22 days ago by finswimmer5.3k
2
votes
1
answer
476
views
1
answer
GaTK reverse select interval list
... I have a file with RNA editing sites which I want to remove from my VCF. I can select all the RNA editing sites with: java GenomeAnalysisTK.jar \ -T SelectVariants \ -R human_g1k_v37.fasta \ -V input.gg.vcf.gz \ -o output.gg.vcf.gz \ -L Human_AG_all_hg19_ ...
gatk intervallist written 12 months ago by Niek De Klein2.4k • updated 12 months ago by Pierre Lindenbaum112k
0
votes
1
answer
599
views
1
answers
Comment: C: Bedtools merge only part of feature that overlaps, not whole feature
... Thanks for the detailed explanation! For others that find this question, this is how I went from ensemble GTF to BED with CHR, start, stop, ensemble gene ID: awk '{if ($3 == "gene") print $0;}' Homo_sapiens.GRCh37.75.gtf \ | bedtools sort -i stdin \ | awk '{print $1 "\t" $4 "\t ...
written 13 months ago by Niek De Klein2.4k
1
vote
2
answers
443
views
2
answers
Answer: A: Get sequences from oligonucleotide probe ids
... The second column is an NCBI nucleotide ID, you can search the nucleotide database for the sequence. For example: https://www.ncbi.nlm.nih.gov/gquery/?term=XM_001122142.1 ...
written 13 months ago by Niek De Klein2.4k
4
votes
1
answer
599
views
1
answer
Bedtools merge only part of feature that overlaps, not whole feature
... I want to merge the genes in a bedfile so that only the parts of the gene that overlap become a new feature. E.g., have this bedfile: 1 pseudogene gene 11869 14412 . + . gene_id "ENSG00000223972" 1 pseudogene gene 14363 29806 . - ...
bedtools bed merge written 13 months ago by Niek De Klein2.4k • updated 13 months ago by Alex Reynolds25k
0
votes
0
answers
864
views
0
answers
Comment: C: Extremely low assigned reads in featureCounts
... Was the sequencing done strand-specific? ...
written 14 months ago by Niek De Klein2.4k
0
votes
1
answer
793
views
1
answers
Answer: A: Shapeit can't open existing file
... Don't know how to delete the question, but turns out `chr1.sample` does not exist, the error was just showing the wrong file. ...
written 22 months ago by Niek De Klein2.4k
0
votes
1
answer
793
views
1
answers
Comment: C: Shapeit can't open existing file
... chr_1.haps.gz: gzip compressed data, was "chr_1.haps", from Unix, last modified: Wed Feb 24 16:13:24 2016 ...
written 22 months ago by Niek De Klein2.4k

Latest awards to Niek De Klein

Popular Question 8 weeks ago, created a question with more than 1,000 views. For How to remove non-unique mapping reads with Hisat?
Scholar 10 months ago, created an answer that has been accepted. For A: How To Install The Ucsc In The Linux Operating System
Great Question 10 months ago, created a question with more than 5,000 views. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Great Question 10 months ago, created a question with more than 5,000 views. For When To Choose Python Over Perl (And Vice Versa)?
Student 10 months ago, asked a question with at least 3 up-votes. For How To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
Popular Question 12 months ago, created a question with more than 1,000 views. For How to remove non-unique mapping reads with Hisat?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Popular Question 22 months ago, created a question with more than 1,000 views. For How To Show More Blast Results Using Biopython?
Popular Question 22 months ago, created a question with more than 1,000 views. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Prophet 22 months ago, created a post with more than 20 followers. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question 22 months ago, created a question with more than 1,000 views. For How to remove non-unique mapping reads with Hisat?
Scholar 22 months ago, created an answer that has been accepted. For A: How To Install The Ucsc In The Linux Operating System
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question 23 months ago, created a question with more than 1,000 views. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Why Gene Regulatory Network Is Sparse?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How To Show More Blast Results Using Biopython?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For When To Choose Python Over Perl (And Vice Versa)?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Windows Cmd Not Responding With Python Blastall 2.2.17
Prophet 2.8 years ago, created a post with more than 20 followers. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1353 users visited in the last hour