User: mrals89

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mrals8950
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Posts by mrals89

<prev • 19 results • page 2 of 2 • next >
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Comment: C: aligning with bacterial genome
... Poly A selection is quite common, but OP didn't mention his protocol. Also, poly-A selection biases your samples away from other human RNA species that don't have the tail. You don't need *any* special protocol for bacterial RNA-seq if you're working in an RNAse free environment. Therefore, bacteria ...
written 2.3 years ago by mrals8950
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Comment: C: fastqc "Too many tiles (>500) so giving up trying to do per-tile qualities since
... When the sequencer takes a high-resolution image of the microchip during each cycle, it records fluorescent intensities across the different channels and therefore each residue/fluorophore. It is physically/chemically possible for background or non-specific flourescence to be present on a site tha ...
written 2.3 years ago by mrals8950
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Comment: C: fastqc "Too many tiles (>500) so giving up trying to do per-tile qualities since
... Hi there, I'm sure you're concerned that there's an error at all, since your invocation of the command was valid and your hoping for the best from your dataset... But you haven't actually told us what you want to *do*. We're guessing that you're just doing routine qc with fastqc and not investigatin ...
written 2.3 years ago by mrals8950
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Comment: C: Fasta File To Sam Conversion
... Wasn't the FASTA format derived from the FAST-A (FAST-P) alignment algorithm? ...
written 2.3 years ago by mrals8950
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Comment: C: Should We Remove Duplicated Reads In Rna-Seq ?
... But are type I/II errors from duplication rates expression/quartile dependent? Coefficient of Variation is often the lowest in the most abundant genes, which are also the genes with the highest probability of duplicates (optical, amplification, or true duplicates) by virtue of the amount of data t ...
written 3.2 years ago by mrals8950
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Comment: C: Unaligned Reads From Bowtie2
... Reading the bowtie2 manual, "These reads correspond to the SAM records with the FLAGS 0x4 bit set and neither the0x40 nor 0x80 bits set." This means that the --un option outputs only unpaired reads, even though it searches for unpaired alignments when reads fail to align either concordantly or disco ...
written 5.9 years ago by mrals8950
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In Paired-End Data, If One Read Of The Pair Is Unmapped, Is That Pair Autmoatically Improper?
... Hello everyone, I have a simple question about generic paired-end Illumina data. If one read of a pair is unmapped, does this automatically mean that the pair is improper and is (un)flagged in a SAM file? Thanks! ...
illumina paired-end samtools sam rna-seq written 6.3 years ago by mrals8950 • updated 5.2 years ago by Biostar ♦♦ 20
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Does Every Read In Paired-End Sam File Have The 0X0001 Flag?
... Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag? Thanks! ...
illumina paired-end samtools sam written 6.3 years ago by mrals8950 • updated 6.3 years ago by Istvan Albert ♦♦ 84k
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Directional Rnaseq: Which Mapping Software For Bacteria?
... Hello Biostars! I am looking for mapping software to analyze directional/strand-specific RNA-seq data from both paired-end and single-end libraries of bacterial transcriptomes. I have considered TopHat for the analysis, since I am aware of its --library-type fr-firststrand option to preserve the di ...
mapping rna-seq written 6.5 years ago by mrals8950

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Does Every Read In Paired-End Sam File Have The 0X0001 Flag?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Directional Rnaseq: Which Mapping Software For Bacteria?

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