User: Mick

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Mick10
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1 week, 5 days ago
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9 months, 1 week ago
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Posts by Mick

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Pipeline BWA aln+samse
... Ah ok, I had no idea you could use the dash that way. Now it makes sense. Thank you! ...
written 19 days ago by Mick10
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Pipeline BWA aln+samse
... Hi I'm trying to pipeline the bwa aln and samse commands. This works: bwa samse reference.fa <(bwa aln reference.fa test.fq) test.fq > test.sam But this doesn't: bwa aln reference.fa test.fq | bwa samse reference.fa test.fq > test.sam Why is that, what is the difference? Thank ...
bwa written 19 days ago by Mick10 • updated 19 days ago by ATpoint29k
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What algorithms are underlying in read cutting tools?
... Hi guys, I had to make my own tool for cutting NGS reads. Because our experimental setup is very unique and we have primers and barcodes in ever changing positions, so I couldn't use anything that's on the market. I wrote it in python and it works really well and finds all the positions, but it isn' ...
next-gen written 4 weeks ago by Mick10
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Comment: C: Call all insertions and deletions in bam file
... I tried bbmap's callvariants today, but it only found around 30 indels, but there should be much more than that. Can anyone please suggest a tool, that outputs all indels in a file? This seems like the most basic task. ...
written 6 weeks ago by Mick10
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Call all insertions and deletions in bam file
... Hi, I have a file with ultra-deep sequencing data of a 100bp genomic region that has been sequenced 1M times. (I have posted about this before). I aligned the reads to the genome with bwa. I'm looking for a tool that will call ALL insertions and deletions without any filtering. I will set my own cu ...
pileup written 6 weeks ago by Mick10
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Comment: C: Merge paired reads for error-correction
... Thank you very much for the quick reply. I will write Brian on sourceforge and see if it can be done. I will also start working on my own script. I'm not a programmer but I think I can put something together. Why do you think it would be better to use the fastq files directly and not the mapped read ...
written 7 weeks ago by Mick10
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Merge paired reads for error-correction
... Hi, i have two fastq files for each of my samples which each contain about 1M reads (one file for forward and one for reverse reads). I have the demultiplexing and cutting of adapters done, so the reads are only genomic sequences. The reads are quite short (~100bp) and cover the same genomic sequenc ...
merge paired-reads written 7 weeks ago by Mick10
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Answer: C: Biopythons PairwiseAligner, ".aligned" attribute doesn't work.
... Hey Joe, thank you so much for the help. It was indeed an issue with an older version of biopython on my system. Apparently I had biopython on my system twice and I updated the wrong installation. Here is the versions and system I used: >>>import sys; print(sys.version) 3.6.7 (de ...
written 4 months ago by Mick10
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Biopythons PairwiseAligner, ".aligned" attribute doesn't work.
... Hey guys, i'm trying to use the Biopython PairwiseAligner as such: from Bio import Align aligner = Align.PairwiseAligner() my_target = "ACTTGATCTTTCGT" my_query = "CTTGATCT" aligner.gap_score = -1 aligner.match = 1 aligner.mismatch = -1 aligner.query_end_g ...
alignment written 4 months ago by Mick10 • updated 4 months ago by Joe16k
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Comment: A: Local and global alignment combined
... Thank you guys for your replys. Thank you for the recommendation of the emboss tool. As i said, right now I'm trying to figure out how exactly these algorithms work, thats why I'm trying to write the code myself but when I start to work on my own pipeline I'll definitely consider using it. So I dec ...
written 4 months ago by Mick10

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