User: drikaul

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drikaul10
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2 years, 5 months ago
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Posts by drikaul

<prev • 13 results • page 1 of 2 • next >
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Comment: C: NCBI Accession Number to Taxonomy ID
... Has anyone tried to download Entrez Direct recently? I'm using the command below, as directed here: https://www.ncbi.nlm.nih.gov/books/NBK179288/ sh -c "$(wget -q ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh -O -)" It keeps erroring out for me giving a bunch of errors, an ...
written 9 weeks ago by drikaul10
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Comment: C: bbmap reference mapping error
... but I checked the bbmap version for both the runs, and it's the same, since we haven't updated our install of bbmap for a few months now. ...
written 12 weeks ago by drikaul10
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Comment: C: bbmap reference mapping error
... Thanks for your response! I saw that, but I'm just confused as to why I would need to re-index my reference fasta each time I run the command on a new sample? Would the error disappear if I first indexed the reference and then ran the command on the pool of samples *without* the "ref=" argument? ...
written 3 months ago by drikaul10
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bbmap reference mapping error
... Hi! I'm trying to map my genomes to the C_glabrata reference genome and I'm having some issues with the backend java. I'm running bbmap.sh (Version 38.58) using the following command: bbmap.sh ref=C_glabrata_CBS138_current_chromosomes.fasta in1= in2= outm=output_sam/_mapped.sam trd=t -Xmx1g ...
java bbmap mapping error written 3 months ago by drikaul10 • updated 3 months ago by ATpoint29k
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Comment: C: Joining vs merging paired ended reads
... yes, I used PEAR for this particular analysis, but have used vsearch in the past too. I'm trying to call OTUs on the merged reads, would joining the non-overlapping reads make sense for that purpose? The way I understand it, this might generate erroneous OTU sequences that would skew downstream clu ...
written 3 months ago by drikaul10
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Comment: C: Joining vs merging paired ended reads
... Thanks, that makes sense and is on the lines of what I was thinking! If by merging the reads, you mean, checking to see the overlap, then yes, I already did that and it's minimal. Haven't tried joining them yet. ...
written 3 months ago by drikaul10
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Comment: C: Joining vs merging paired ended reads
... The idea is to call OTUs on them, so I'm trying to figure out what the best way is to make use of the forward and reverse reads since the overlap is minimal. For now, I'm leaning more towards just using the forward reads, since their quality is pretty okay in comparison, but I was just wondering, if ...
written 3 months ago by drikaul10
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Joining vs merging paired ended reads
... Hi community! I have paired-ended amplicon sequences for a batch of samples, with very little overlap (<10%). Conceptually, I was wondering if it makes sense to **join** the forward and reverse read to generate a single read for downstream processing, instead of interleaving/merging them to ge ...
merging paired-ended sequencing written 3 months ago by drikaul10 • updated 3 months ago by h.mon29k
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Comment: C: which tool is used for separating forward and reverse from paired end fastq
... But this would not work on local files that haven't been downloaded from SRA, correct? ...
written 8 months ago by drikaul10
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Comment: C: Interproscan sequence classification
... Thanks for your response! Yes, it's a metaproteome sample, and I'm trying to run both blastp and interproscan to see if there is a difference in the results. But I'll take your advice and stick to protein domain annotations from interproscan, instead of trying to retrieve taxonomic info. ...
written 8 months ago by drikaul10

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