User: biogirl04

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biogirl040
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Posts by biogirl04

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Bowtie2 filter by alignment score
... Hi, Is there a way I can get only reads with an alignment score of greater than -5 in bowtie2 alignment? Thanks! ...
gene next-gen alignment rna-seq snp written 27 days ago by biogirl040
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Bowtie2 Alignment Score Meaning
... Hi, I ran an alignment on Bowtie2 and in the output of the SAM file, I understand that there is an AS tag that signifies Alignment Score. I know that 0 is a perfect match but some of the scores I'm getting are -6, -12, -18. How many points exactly are reduced for mismatches, INDELS, and gaps? How ...
rna-seq bowtie written 5 months ago by biogirl040 • updated 5 months ago by Devon Ryan88k
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Comment: C: How to display mismatched sequences from alignment when using Biopython
... Is there a way to make this faster? It seems really slow right now. ...
written 7 months ago by biogirl040
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Tophat2 Aligning extremely short reads
... Hi, Can tophat2 align reads with lengths = 6bp? If not, which tool can? Thanks! ...
tophat alignment rna-seq sequencing written 7 months ago by biogirl040 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: HISAT2 relaxing parameters?
... Oops, sorry I didn't clarify this before. This is Oxford Nanopore Sequencing data. ...
written 7 months ago by biogirl040
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Comment: C: Tophat2 Error gzip pipe broken? zipped file empty?
... I don't completely remember but I either did: `sudo apt-get install tophat` or I downloaded from https://ccb.jhu.edu/software/tophat/index.shtml ...
written 7 months ago by biogirl040
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Comment: C: HISAT2 relaxing parameters?
... Hi, Yes, I understand that. However, I am using the default and am not getting what I expected. I just switched from using tophat2 to hisat2 and I know that hisat2 is much more sensitive. Is there a similar option on hisat2 to change the --read-mismatches, --read-edit-dist, and --read-gap-length? ...
written 7 months ago by biogirl040
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Comment: C: Tophat2 Error gzip pipe broken? zipped file empty?
... Thanks for your help! This is the command that I had run: tophat2 -r 300 -o this1_out readsfastaindex/readsF orf.fastq For some reason, no matter what I do, I keep getting the same error as above. Any ideas? ...
written 7 months ago by biogirl040 • updated 7 months ago by h.mon23k
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HISAT2 relaxing parameters?
... Hi, It's my first time using HISAT2 and the options have gotten me all confused. How can I run HISAT2 such that I increase the number of mapped reads by relaxing the parameters? Essentially, how can I increase the number of mismatches, etc allowed (which options do I need to use and how)? Thanks s ...
mismatches alignment mapping rna-seq hisat2 written 7 months ago by biogirl040
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Tophat2 Error gzip pipe broken? zipped file empty?
... Hi everyone, I have the following error when using Tophat2: readlink: illegal option -- f usage: readlink [-n] [file ...] [2018-07-06 11:36:32] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2018-07-06 11:36:32] Checking for Bowtie Bowtie ...
tophat2 alignment rna-seq bowtie gzip written 7 months ago by biogirl040 • updated 7 months ago by h.mon23k

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