User: DNAngel

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DNAngel20
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Posts by DNAngel

<prev • 32 results • page 1 of 4 • next >
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Do the lowercase bases seen in BAM files need to be reverse complemented in consensus?
... I'm creating consensus sequences using a custom script but I am unsure if lowercase bases (the bases that are on the reverse strand) are already reverse complemented, or they need to be reverse complemented? In IGV, when I see reads aligned to a position and I have a mix of A (forward reads), and ' ...
bam written 9 days ago by DNAngel20 • updated 9 days ago by Devon Ryan87k
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Comment: C: How to count the total aligned bases in BAM?
... Hi, this sounds like something I need as well. Does this count the actual number of reads that contain a particular base or just how many reads aligned at that position? For example at position 1 if I know I have 100 reads aligned there, would it tell me I have 50 A's, 25 a, 25 C? Something like tha ...
written 10 days ago by DNAngel20
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Comment: A: How to create consensus from bam file without IUPAC code?
... Did you find out how to create the consensus sequences without IUPAC codes? I'm having the same problem using samtools and bcftools. ...
written 14 days ago by DNAngel20
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Comment: C: How to get consensus fastq file without IUPAC codes using vcfutils?
... I can create consensus sequences now, I just cannot get them to not include IUPAC codes so I do think they are different questions. ...
written 14 days ago by DNAngel20
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Comment: C: How to get consensus fastq file without IUPAC codes using vcfutils?
... Tried it but it didn't work no output consensus file would even be created for me to check. It definitely runs (no weird errors pop up) and something happens but it does not give me the output. I didn't understand how to use mosdepth, it seemed like I would have to relearn quite a bit when I was at ...
written 14 days ago by DNAngel20
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(Closed) How to get consensus fastq file without IUPAC codes using vcfutils?
... The only code that appears to work for me when I want to generate consensus sequences have been: samtools mpileup -Q 20 -q 20 -d 5000 -uf ref.fa sorted.bam | bcftools call -c | vcfutils.pl vcf2fq -d 10 -Q 20 -l 1 > consensus_output.fq However, I don't need ambiguity and almost every spot in ...
consensus bcftools samtools written 14 days ago by DNAngel20
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Comment: C: Confused about how to generate a consensus sequence after bwa
... Yes that is me! Thank you I will try this as well. Also, I think I may have gotten it with bcftools using call as you suggested but using -d 10 and -Q 20 settings to ensure high quality base calls are kept. And that (to me right now at least) makes the consensus only contain the high quality base ca ...
written 27 days ago by DNAngel20
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Comment: C: Ngs Question ~ Consensus
... Coming in 4 year later, I've tried these lines of code for my single-end BAM file but the consensus sequence fills in gaps with bases from the reference.fasta file. Is there a way to just get a consensus of the BAM file or even the mpileup file to also keep gaps where there was no depth of coverage ...
written 28 days ago by DNAngel20
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Comment: C: Confused about how to generate a consensus sequence after bwa
... Hi, I know you mentioned to me earlier in another site that bcftools consensus will fill in gaps with bases from the reference...but I know from other scripts where colleagues have worked with paired-end data that this is not true. They were able to get the consensus sequence of their species1.bam f ...
written 28 days ago by DNAngel20
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Comment: A: Confused about how to generate a consensus sequence after bwa
... I've ran into a new issue, now I cannot create a consensus sequence at all and I don't understand why. I have my indexed (from bwa) reference files and my sorted alignment bam files for 30 species in the same directory. I am trying to make consensus sequences of them all. I am even trying to do thi ...
written 4 weeks ago by DNAngel20

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Scholar 5 weeks ago, created an answer that has been accepted. For A: How to save trimmomatic terminal summary to an output file?

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