User: michaela_boell

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Posts by michaela_boell

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Comment: C: Mapping Issues with Bowtie2
... It should be exactly the other way around, are sure you did not mix up which one is which? ...
written 3.8 years ago by michaela_boell70
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Comment: C: Which Read-Depth is Needed to Find Insertions?
... We decided on PE reads because we suspected that there cases where additional fragments are inserted between the T-DNA (something in principle like a transposon) and the genome. This makes the border larger, in a way. The tool I used was Bowtie2 on a reference that included the T-DNA sequence as an ...
written 3.8 years ago by michaela_boell70
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Comment: C: Which Read-Depth is Needed to Find Insertions?
... Roughly 900bp. I actually have a dataset of 75 bp mate-pair PE reads but I am investigating different alignment approaches. ...
written 3.8 years ago by michaela_boell70
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Comment: C: Which Read-Depth is Needed to Find Insertions?
... Thank you very much! What is your estimate, would you try to find insertions that are long, but you only care about the ends, with short reads, 50 bp or 75 bp SE ? ...
written 3.8 years ago by michaela_boell70
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Which Read-Depth is Needed to Find Insertions?
... Hello, According to a review by D Sims et al [1], the required average mapped depth is 35× in order to detect heterozygous SNVs and indels in resequencing studies. I wonder why it is so high. Is this only due to the non-uniformity of read-depth? And would this be higher if one sets out to find larg ...
alignment sequencing written 3.8 years ago by michaela_boell70 • updated 3.8 years ago by Brian Bushnell17k
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Comment: C: Extracting Paired-End Reads Sitting In Different Chromosomes
... A version that allows the reversion to bam includes the header: samtools view -F 14 -h infile.bam | grep -v " = " > outfile.sam reversion to bam: samtools view -b outfile.sam > finalout.bam ...
written 3.8 years ago by michaela_boell70
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Comment: C: Extracting Paired-End Reads Sitting In Different Chromosomes
... No, since identical RNAME and RNEXT are excluded. Or am I missing something? ...
written 3.8 years ago by michaela_boell70
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Comment: C: BAM to FASTQ
... This sounds quite good, actually. My project is to find out T-DNA insertions. T-DNAs are principally similar to transposons; they are short gene casettes that are inserted randomly (in a plant genome via Agrobacterium mediated transformation). I want to find out every T-DNA insertion in several da ...
written 3.8 years ago by michaela_boell70
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Comment: C: BAM to FASTQ
... Useful post: https://www.biostars.org/p/56246/#228516 ...
written 3.8 years ago by michaela_boell70
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Comment: C: How To Filter Mapped Reads With Samtools
... but with -f 4 only the mates are extracted that did not map, leaving out the part that did map ( -f 8). Or am I wrong? By this the information about pairing is lost, which is the valuable thing about paired-end datasets. There are cases, where one mate maps to one reference, but both do map to anot ...
written 3.8 years ago by michaela_boell70

Latest awards to michaela_boell

Popular Question 3.8 years ago, created a question with more than 1,000 views. For Error: Could not find Bowtie 2 index files (Reference.fas.*.bt2l)
Supporter 3.9 years ago, voted at least 25 times.

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