User: Steffi

gravatar for Steffi
Steffi570
Reputation:
570
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Trusted
Location:
Germany
Last seen:
5 years, 3 months ago
Joined:
8 years, 9 months ago
Email:
s**************@gmail.com

Posts by Steffi

<prev • 46 results • page 1 of 5 • next >
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Variation Statistics on bam file over all reads
... Hi, I have a bam file from RNA-Seq data and I would like to have some overview statistics on the occurring variations (number of mismatches, which transitions exactly, number of deletions/insertions..) However, rather than computing this on the pile-up-level (coverage-level), I would like to have ...
bam pysam written 5.7 years ago by Steffi570
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Job: PhD positions in Computational Biology, PhD Programme in Mainz, Germany
... PhD positions in Computational Biology The International PhD Programme in Mainz invites applications for Computational Biology/Bioinformatics. Several projects are available including data mining, -omics data analysis and systems biology. Prof. Miguel Andrade (Computational Biology and Data Mini ...
job computational biology written 5.8 years ago by Steffi570 • updated 5.8 years ago by Istvan Albert ♦♦ 84k
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Wgsim - Distribution Of Reads Along The Genome
... Does anybody how wgsim or simNGS chose the distribution of the reads along the genome? Randomly (so uniformly?) ...
simulation written 8.1 years ago by Steffi570 • updated 8.1 years ago by Botond Sipos1.7k
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Sample Sam File
... Hi, I have a sam file which contain alignments of about 30 million reads. I just would like to randomly sample e.g. 1 million alignments out of my sam file. Whats the best way to do this? Anything already available in any kind of toolkit? Or bash scripting? Or Perl? thanks a lot, Steffi ...
sam random written 8.2 years ago by Steffi570 • updated 6.0 years ago by Biostar ♦♦ 20
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Comment: C: Filter Paired-End Sam File For Xt:A:U
... Thanks a lot! I appreciate your help! ...
written 8.3 years ago by Steffi570
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Comment: C: Filter Paired-End Sam File For Xt:A:U
... This does not work, because a read can still have the flag of being properly mapped but having lost its mate at the grep-step before... ...
written 8.3 years ago by Steffi570
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Comment: C: Filter Paired-End Sam File For Xt:A:U
... But this would (possibly) destroy the pairs: It might occur that one read of a pair is mapped with XT:A:U but the other not. In that case only one read of the pair would be retained. ...
written 8.3 years ago by Steffi570
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Filter Paired-End Sam File For Xt:A:U
... Dear all, I have a sam file (BWA output, paired-end reads). I would like to retain only reads which are "properly paired". This I would do by: samtools view -f 0x002 file.sam > file_filtered.sam Additionally I would like to retain only those pairs of reads where both reads have the XT:A:U tag. ...
filter paired-end sam bwa written 8.3 years ago by Steffi570 • updated 6.7 years ago by Biostar ♦♦ 20
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Brlmm-P Cluster Centers
... When I call genotypes with apt-probeset-genotype (Affymetrix Powertools, brlmm-p method), how do I get the cluster centers for each SNP? Best regards, Stefanie ...
affymetrix snp written 8.3 years ago by Steffi570
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Papers Comparing Different Protocols For Next Gen Seq
... Hi, I would be interested in papers comparing different protocols (e.g. different priming methods, different fragmentation methods, etc.) for DNA or RNA seq. I know the paper from Levin et al (Comprehehnsive comparative analysis of strand-specific RNA sequencing methods). Does somebody know about ot ...
next-gen sequencing written 8.3 years ago by Steffi570 • updated 8.3 years ago by Sravanthi Davuluri40

Latest awards to Steffi

Appreciated 5.4 years ago, created a post with more than 5 votes. For Sample Sam File
Great Question 5.4 years ago, created a question with more than 5,000 views. For Duplicated Reads In Rna-Seq Experiment
Appreciated 8.0 years ago, created a post with more than 5 votes. For Sample Sam File
Appreciated 8.0 years ago, created a post with more than 5 votes. For Conference On Statistics Of Ngs Data
Good Question 8.0 years ago, asked a question that was upvoted at least 5 times. For Conference On Statistics Of Ngs Data
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Sample Sam File
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Duplicated Reads In Rna-Seq Experiment
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Q-Pcr For Rna-Seq Data
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Filter Paired-End Sam File For Xt:A:U
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Bwa: "Xt:A:U" And Mapq Of 0 At The Same Time
Student 8.0 years ago, asked a question with at least 3 up-votes. For Sample Sam File
Student 8.0 years ago, asked a question with at least 3 up-votes. For Duplicated Reads In Rna-Seq Experiment
Student 8.0 years ago, asked a question with at least 3 up-votes. For Bwa: "Xt:A:U" And Mapq Of 0 At The Same Time
Student 8.0 years ago, asked a question with at least 3 up-votes. For Conference On Statistics Of Ngs Data

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