User: Niek De Klein
Niek De Klein • 2.4k
- Reputation:
- 2,440
- Status:
- Trusted
- Location:
- Netherlands
- Last seen:
- 2 months, 4 weeks ago
- Joined:
- 8 years, 6 months ago
- Email:
- n**********@gmail.com
Posts by Niek De Klein
<prev
• 253 results •
page 1 of 26 •
next >
0
votes
2
answers
3.2k
views
2
answers
... Haven't tested for edge cases but can try something like this
def consensus(*sequences):
if(len(sequences) <= 1):
raise RuntimeError('Only '+str(len(sequences))+' sequences given, need at least 2')
consensus_sequence = ''
for index, amino_acid in ...
written 4 months ago by
Niek De Klein • 2.4k
0
votes
0
answers
351
views
0
answers
... The problem was in the .dict file, which was apparently made using the gzipped reference genome fasta, while the CRAM was made using the unzipped reference genome fasta. I remade the .dict file with the unzipped genome fasta file and now it works.
Thanks for the help! ...
written 4 months ago by
Niek De Klein • 2.4k
0
votes
0
answers
351
views
0
answers
... head -n30 /apps/data//ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_24/GRCh38.p5.genome.fa.fai
chr1 248956422 8 60 61
chr2 242193529 253105712 60 61
chr3 198295559 499335808 60 61
chr4 190214555 700936301 60 61
chr5 181538259 894321107 60 61
chr6 170805979 10788 ...
written 4 months ago by
Niek De Klein • 2.4k
0
votes
0
answers
351
views
0
answers
... Yes the path exists and the double / is not a problem. If the reference file can not be found it gives this error: `Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: /fake/path/genome.fa` ...
written 4 months ago by
Niek De Klein • 2.4k
0
votes
0
answers
351
views
0
answers
... This is a cross-post from here: https://gatkforums.broadinstitute.org/gatk/discussion/13395/sequences-at-index-0-dont-match-but-using-the-same-reference-genome#latest
I am trying to run CollectMultipleMetrics from Picard tools on a CRAM file but I get an "Sequences at index 0 don't match, but usin ...
written 4 months ago by
Niek De Klein • 2.4k
0
votes
1
answer
973
views
1
answers
... 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 6 months ago by
Niek De Klein • 2.4k
0
votes
1
answer
973
views
1
answers
... Thanks, I'm testing this now and seeing how it compares to removing secondary aligned reads ...
written 6 months ago by
Niek De Klein • 2.4k
2
votes
1
answer
973
views
1
answer
... 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 ...
written 6 months ago by
Niek De Klein • 2.4k
• updated
6 months ago by
finswimmer ♦ 11k
2
votes
1
answer
642
views
1
answer
... 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_ ...
written 18 months ago by
Niek De Klein • 2.4k
• updated
18 months ago by
Pierre Lindenbaum ♦ 117k
0
votes
1
answer
773
views
1
answers
... 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 19 months ago by
Niek De Klein • 2.4k
Latest awards to Niek De Klein
Popular Question
3 months ago,
created a question with more than 1,000 views.
For biomaRt LPR region to position giving different results than I expect (using R)
Great Question
4 months ago,
created a question with more than 5,000 views.
For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How to remove non-unique mapping reads with Hisat?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For How to remove non-unique mapping reads with Hisat?
Scholar
16 months ago,
created an answer that has been accepted.
For A: How To Install The Ucsc In The Linux Operating System
Great Question
16 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
16 months ago,
created a question with more than 5,000 views.
For When To Choose Python Over Perl (And Vice Versa)?
Student
16 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
18 months ago,
created a question with more than 1,000 views.
For How to remove non-unique mapping reads with Hisat?
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: Is Conversion From Colorspace To Base Space Lossy?
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For What Is (Or How To Find Out) The Meaning Of Error Code -1073741510 From Local Blast 2.2.25+?
Good Question
2.3 years 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
2.3 years ago,
created a question with more than 1,000 views.
For How to remove non-unique mapping reads with Hisat?
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For How To Show More Blast Results Using Biopython?
Prophet
2.3 years ago,
created a post with more than 20 followers.
For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: How To Install The Ucsc In The Linux Operating System
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Biopython Ncbistandalone Blastall Gives Different Result Than Calling Blastall Directly From Cmd
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: Is Conversion From Colorspace To Base Space Lossy?
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For How To Show More Blast Results Using Biopython?
Appreciated
2.6 years ago,
created a post with more than 5 votes.
For A: Why Gene Regulatory Network Is Sparse？
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For When To Choose Python Over Perl (And Vice Versa)?
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Windows Cmd Not Responding With Python Blastall 2.2.17
Epic Question
3.1 years ago,
created a question with more than 10,000 views.
For When Using Heatmap.2 From R To Make A Heatmap Of Microarray Data, How Are The Genes Clustered?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2166 users visited in the last hour