User: Aragion

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Aragion0
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Posts by Aragion

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Comment: C: Metatranscriptomic reads alignment and assembly
... Tnahk you for answer! The proble is that Trinity contigs BLAST against various non-viral sequences even when I chose virus database. Perhaps it is because this tool assembles reads as eukariotic transcripts with exones but not as RNA-genomes. May be I should try to increase the contig length in Trin ...
written 6 months ago by Aragion0
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Metatranscriptomic reads alignment and assembly
... Hello. I have a set of metatranscriptomic Illumina paired-end reads. I need to align them against the database of plant virus genomes (about 55000 sequences) and calculate coverage for each reference. How can I solve the problem? It is also necessary to assemble these reads de novo. I've tried Tri ...
metatranscriptome assembly rna-seq written 6 months ago by Aragion0 • updated 6 months ago by Jennifer Hillman Jackson23k
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Assembly of metatranscriptomic data with reference
... Hello. I have a set of reads produced by metatranscriptomic cDNA sequensing of the total RNA sample. I need to assemble the RNA-virus genome, which was detected in this sample by the PCR-analysis, using reference sequence from GenBank and the reads. I have never encountered such a problem so can you ...
assembly written 10 months ago by Aragion0 • updated 10 months ago by Jennifer Hillman Jackson23k
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Low mapping of paired-end reads with tophat2
... Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage if mapped reads is almost 0% Left reads: Input: 9526882 Mapped: 224 ( 0.0% of input) of these: 22 ( 9.8%) have multiple alignments (0 have >20) Right reads: Input: 9526882 Mapped: 23 ...
tophat written 12 months ago by Aragion0 • updated 11 months ago by Jennifer Hillman Jackson23k

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