User: hannahfreund3

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Posts by hannahfreund3

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Comment: C: bbduk truncated fastq file according to FastQC - help?
... That was my thought, and it's such a low % of the R2 reads. Thanks for the input! ...
written 17 days ago by hannahfreund30
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bbduk truncated fastq file according to FastQC - help?
... I was able to succeessfully remove adapters from my PE 150bp x 2 reads using bbduk.sh, but I kept seeing that I had a long string of Gs in my R2 sequences (~ 0.1% of my R2 reads). I reran the original fastq files with bbduk to remove the string of Gs, and this worked for most of my PE files except ...
pe bbduk metagenome fastqc written 17 days ago by hannahfreund30 • updated 17 days ago by swbarnes28.8k
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Comment: C: Losing most PE reads using Cutadapt on 150bp PE metagenomes
... Thank you for pointing that out, you're right. I am trying to use bbduk to remove the adapters w/ their respective indexes (before I was clearly just looking for indexes) - hopefully this works. Do you have another recommendation for removing the adapters with their indexes? FastQC says there's a ...
written 20 days ago by hannahfreund30
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Losing most PE reads using Cutadapt on 150bp PE metagenomes
... Hi everyone, I am using cutadapt to cut some adapters on my PE, metagenome reads (150bpx2, Illumina NovaSeq). Here is my code: for i in *_R1_001.fastq; do SAMPLE=$(echo ${i} | sed "s/_R1_\001\.fastq//") echo ${SAMPLE}_R1_001.fastq ${SAMPLE}_R2_001.fastq/n cutadapt ...
pairedend pe metagenome shotgun cutadapt written 24 days ago by hannahfreund30 • updated 24 days ago by h.mon31k
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Should I merge, then trim PE reads before multiple sequence alignment?
... Hi everyone! I have a set of demultiplexed fungal ITS1 reads, and I'd like to run a multiple sequence alignment with these R1 and R2 reads using MUSCLE. I've used MUSCLE with metagenomic shotgun data, not amplicon data, so I am not sure about how to preprocess my sequences before the MSA. Should ...
alignment #its1 #amplicon #msa written 8 months ago by hannahfreund30 • updated 8 months ago by h.mon31k

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