User: 7ehuang

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7ehuang0
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Posts by 7ehuang

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Comment: A: BwaMemIndexImageCreator fails to generate reference.img file
... maybe you need to request more memory? ...
written 5 days ago by 7ehuang0
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Comment: C: megablast returns hits not found by blastn?
... Sorry about that, I mistyped. I meant to say I got 0 hits for blastn and thousands of matches for megablast (edited the original post). This is why I'm confused, because I also expected getting more matches with blastn than megablast. When I tried -task 'blastn-short', I also got 0 matches. ...
written 9 days ago by 7ehuang0
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megablast returns hits not found by blastn?
... Hi all, It is my understanding that blastn is more sensitive (and thus finds more hits) than megablast (see [here][1] and [here][2]). However, when I compared my results from running blastn vs. megablast with the same exact inputs and parameters, I got 0 hits for blastn and thousands of matches for ...
megablast e-value blastn blast+ query written 9 days ago by 7ehuang0
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Comment: C: jellyfish kmer counting discrepancy
... Oh, this is great! Exactly the tool I need. Thank you very much. ...
written 11 days ago by 7ehuang0
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Comment: C: jellyfish kmer counting discrepancy
... Now that you mention it, I see that the 31mers I'm running into this problem for all have duplications of some kmer within them. Thank you very much! ...
written 11 days ago by 7ehuang0
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Comment: C: jellyfish kmer counting discrepancy
... Thank you both for your responses! Since I am counting kmers in a genome, the reverse-complement of a kmer shouldn't be considered equivalent to it, so when I ran kmercountexact.sh, I used the rcomp=f parameter. Not considering a kmer and its reverse-complement equivalent is the default behavior f ...
written 11 days ago by 7ehuang0
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jellyfish kmer counting discrepancy
... Hi all, I am using jellyfish to count kmers of length 31 that appear in a viral genome sequence. These were the commands I ran: jellyfish count -m 31 -s 154675 -t 10 NC_001798.fa # the -s parameter is based on the size of the NC_001798 genome jellyfish dump mer_counts.jf > mer_counts_ ...
genome count kmer rna-seq jellyfish written 11 days ago by 7ehuang0 • updated 11 days ago by Istvan Albert ♦♦ 81k
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ViromeScan trimBWAstyle.usingBam.pl parameters
... Hi all, I have been trying to use the ViromeScan software (https://sourceforge.net/projects/viromescan/) to detect viral sequences in RNA-Seq samples. The pipeline utilizes the perl script trimBWAstyle.usingBam.pl with the parameters -q 3 -o 65 -l 60. According to the documentation for trimBWAstyl ...
metagenomics bam rna-seq viromescan virus written 4 weeks ago by 7ehuang0

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