User: cschu181

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cschu181670
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Posts by cschu181

<prev • 116 results • page 1 of 12 • next >
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Comment: C: What tools are proper to preprocess FASTA coming from Velvet assembler into the
... What do you mean with duplication error? Duplicate sequences? Duplicate sequence ids? ...
written 1 day ago by cschu181670
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Comment: C: Is there something wrong with my Indel Calling protocol?
... Have you tried an established pipeline, such as CRISPResso to compare the results? Or try playing with the GAP penalties of bwa mem, maybe your reads get dropped due to low scoring? ...
written 2 days ago by cschu181670
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Comment: C: Run CIRI program directly from BWA-mem alignment
... You could try process substitution for the input sam `perl CIRI.pl -I <(put your bwa mem call (or even bwa mem | samtools pipeline) here) -O outfile -F ref.fa (-R ref_dir/) -P`. It is not guaranteed to work, though, especially if CIRI makes multiple passes over the sam file. ...
written 7 days ago by cschu181670
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Comment: C: What is the input file for kraken to create krona plots?
... Can you tell us where you have tried searching? The official documentation at https://ccb.jhu.edu/software/kraken/MANUAL.html is quite well written and provides everything that you need to get started with kraken. ...
written 10 days ago by cschu181670
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Comment: C: SNP analysis of Allotetraploid genome
... Yes, and in GATK Haplotype Caller you can leave the default setting of 2. ...
written 16 days ago by cschu181670
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Comment: C: SNP analysis of Allotetraploid genome
... In the case of allotetraploids, you're not dealing with 4 copies of the same chromosome. Instead, you treat A and D chromosomes as different entities, with 2 copies each. In practice, this means that if your SNP Caller allows you to set ploidy, then you can set it to (or leave it at) diploid. For, s ...
written 17 days ago by cschu181670
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Comment: C: Trimmomatic non-conventional adaptors and error
... Could you try running that with only single spaces between the arguments, i.e. remove all the backslashes and newlines? It kinda looks as if Trimmomatic mistakes one of the output files as trimming module. Now the question is, why? ...
written 5 weeks ago by cschu181670
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Comment: C: get final output from Trimmomatic
... What I meant is: your output that you want to parse should be independent of the -trimlog option. That option will tell you for *each read* how it was processed. I just tested this on a Trimmomatic (v 0.36) run. You will get your output without -trimlog. You just need to redirect the output of Trimm ...
written 6 weeks ago by cschu181670
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Comment: C: get final output from Trimmomatic
... Are you sure that this "Input Reade Pairs..." string is not part of the standard output without -trimlog option? I don't have time to check now. The -trimlog itself you definitely want to avoid. You can easily count the reads from the FASTQ files: lines=$(wc -l fastq_file) reads=$((lines/4) ...
written 6 weeks ago by cschu181670
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Comment: C: get final output from Trimmomatic
... Assuming the Trimmomatic output is in a file named "trimmomatic_output", one solution would be: both=$(grep "^Input Read Pairs" trimmomatic_output | sed "s/.\+(\([0-9.]\+\)%).\+/\1/") echo $both 1.11 ...
written 6 weeks ago by cschu181670

Latest awards to cschu181

Appreciated 24 days ago, created a post with more than 5 votes. For A: Getting PFAM database
Scholar 5 months ago, created an answer that has been accepted. For A: Simple python script to convert ambiguity codes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Simple python script to convert ambiguity codes
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Scholar 7 months ago, created an answer that has been accepted. For A: Simple python script to convert ambiguity codes
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Scholar 9 months ago, created an answer that has been accepted. For A: Simple python script to convert ambiguity codes
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