User: cook284

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cook2840
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Posts by cook284

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Humann2 for metatranscriptomic data
... I have some metatranscriptomic data from a community consisting of one green alga and a mixed population of bacteria. I want to annotate the transcripts from both eukaryotic and prokaryotic community members and get pathway abundance measures so that I can compare the metabolic activities between tw ...
metatranscriptomics humann2 rna-seq written 4 months ago by cook2840
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Comment: C: kmergenie to estimate genome size and then sequencing coverage
... Hi again Brain. This is what NCBI ask for: "The estimated base coverage across the genome, eg 12x. This can be calculated by dividing the number of bases sequenced by the expected genome size and multiplying that by the percentage of bases that were placed in the final assembly. More simply it is th ...
written 15 months ago by cook2840
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Comment: C: kmergenie to estimate genome size and then sequencing coverage
... Hi Brian, Thank you. I misunderstood what was required as the % bps placed in the final assembly (hence calculating it as number of bps in the assembly as a % of total number of bps sequenced). I have now mapped the reads as below: $ bowtie2 -p 6 -f -x Str113_genomeidx -1 Strain113_S52_R1_001.fasta ...
written 15 months ago by cook2840
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Comment: C: kmergenie to estimate genome size and then sequencing coverage
... Hi, Yes this genome size is similar to that of other closely related species on NCBI. It was more the method for calculation of coverage I was concerned with. ...
written 15 months ago by cook2840
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kmergenie to estimate genome size and then sequencing coverage
... Hi all. I'm in the process of uploading a draft bacterial genome assembly to NCBi. NCBI asks that you give a coverage estimate based on #bps sequenced/ expected genome size x % of bps placed in final assembly. I have calculated this using the kmergenie estimate for expected genome size as this is a ...
kmergenie genome size coverage written 15 months ago by cook2840 • updated 15 months ago by Rayan Chikhi1.2k
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Bacterial signal in metatranscriptome data
... Hi all. I have some RNA-Seq data from the sequencing of a green algae in co- culture with a bacterium. The bacterial cell numbers were reported to be in a 50:1 ratio with the green algae. However, only ~7% of the reads are ascribed to bacteria, the rest are algae/ plant. I have argued myself silly a ...
meta rna-seq transcriptome written 16 months ago by cook2840
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IDBA- MTP input file
... Hi all, I am trying to use the IDBA-MTP pipeline to assemble some metatranscriptome data. I have done some digging online to no avail to find out what exactly the assembler is expecting as input for the -p prot_filepath please? Charlotte ...
assembly rna-seq metatranscriptome written 17 months ago by cook2840 • updated 4 months ago by germelcar20

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