User: gufernandez10

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Posts by gufernandez10

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Comment: C: bowtie "Saw ASCII character -54 but expected 33-based Phred qual." after -Q 33 f
... artemis perform easily the RPKM, anyway i follow your advice and perform the count with featureCounts and then estimate the RPKM manually. thanks for reply again. ...
written 3.1 years ago by gufernandez1010
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Comment: C: bowtie "Saw ASCII character -54 but expected 33-based Phred qual." after -Q 33 f
... maybe yes, but the only additional option described in fastx to solve problems with encoded is -Q 33 and if i skip this option get the follow :fastx_reverse_complement: Invalid quality score value (char '.' ord 46 quality value -18) on line 8", so i don't know exactly what its the source of trouble. ...
written 3.1 years ago by gufernandez1010
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Comment: C: bowtie "Saw ASCII character -54 but expected 33-based Phred qual." after -Q 33 f
... Hi, thanks for reply. I should reverse complement the fastq file because i tried to get RPKM using artemis from a paired-end alignment, but artemis don't handle the representation very well of pair-end alignment, showing something like a mirror as a representation of that. So, one option that i have ...
written 3.1 years ago by gufernandez1010
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bowtie "Saw ASCII character -54 but expected 33-based Phred qual." after -Q 33 fastx reverse complement
... hi, I'm working with RNA-seq data. I reverse complemented sequences in a fastq file using fastx reverse complement function adding the -Q 33 option. Without this option I got this error: "fastx_reverse_complement: Invalid quality score value (char '.' ord 46 quality value -18) on line 8". Now when I ...
fastx rna-seq bowtie written 3.1 years ago by gufernandez1010
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Comment: C: Problem to align colorspace data in bowtie1
... do you know some tool that make a good transformation of solid data to illumina data? ...
written 3.7 years ago by gufernandez1010
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Answer: A: Problem to align colorspace data in bowtie1
... thank for answer.    I tryed run fastqc but i belive that my file is to big because just charge the 35% of the file and keep stoped and i don't know a tool better than fastqc to take a look to colorspace file. I dont think that the problem its the hardware because is a server over 30GB of ram.  I j ...
written 3.7 years ago by gufernandez1010
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Problem to align colorspace data in bowtie1
... Hi i download a data set from SRA database get from ABI Solid 4 System platform, i used the following command: bowtie ../../Syne -C -S -p 7 --best --strata -m 1 ../stdc_1.fastq >stc_1.sam to get uniquely mapped, but after a minuts running the alingment abort showing: Reads file contained a patte ...
alignment colorspace bowtie rna-seq written 3.7 years ago by gufernandez1010 • updated 2.2 years ago by xiaoshen199309010
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Comment: C: What tools can use to find RNA modification sites?
... thanks it's a good aproximation and useful in mm10 that i'm studying, but i'm looking for something more specific, maybe a software that find this specific modification sites. Now i'm find a software names HAMR (high trhoughput....) that find modified nucleotides.  ...
written 4.0 years ago by gufernandez1010
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fastx issue with reverse_complement , change in overepresented sequences
... HI i'm working with fastx to get the reverse_complement from fastq file downloaded from sra and separated by sra-toolkit. My problem is after using fastx reverse_complement , the overepresented sequences identified by fastqc change. I would expect the number of reads overrepresented in the two file ...
fastq fastx rna-seq written 4.0 years ago by gufernandez1010
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Answer: A: Some protocol or pipeline to find sRNA using RNA-seq data in with a reference ge
... Hi thanks for reply and sorry excuse my tardiness. I dont understand exactly to what do you refer about tRNA presence, see tRNA where, when i detect some high coverage regions?. Additionaly i'm looking for a workflow or pipeline "tested" to find them, because now i'm doing something similar but i do ...
written 4.1 years ago by gufernandez1010

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