User: bdy8

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bdy850
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Posts by bdy8

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Salmon BAM target length different to FASTA file sequence length
... To provide an answer to this query, it seems STAR is doing something during the indexing step which is causing a slight mismatch for 23 of the transcripts. If you read above replies to the original post you will see the workflow that was done to identify the problem transcripts and the various lengt ...
written 21 days ago by bdy850
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Comment: C: Salmon BAM target length different to FASTA file sequence length
... Good morning Apologies had to completely switch tack to another project. And yes, I did all the comparisons with aligning to STAR. STAR gets more but then when quanting with salmon it becomes less and what is expected. As you recommend I am going to follow up with Alex today or tomorrow :). Thank ...
written 21 days ago by bdy850
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Comment: C: Salmon BAM target length different to FASTA file sequence length
... Hi Rob TX = transcriptome Just some more information for you, after some more digging and checking I believe it is STAR that is the culprit. I checked all TX lengths in my STAR bam file (B), mrna_tx supplied with genome (M) and gffread generated TX using same inputs for generating STAR index (G). ...
written 4 weeks ago by bdy850
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Comment: C: Salmon BAM target length different to FASTA file sequence length
... Good morning Rob :) First of all thank you for the in depth response ! Thankyou for the more in depth on the CIGAR, i get this a bit more now. I am guessing this is a new implementation as using the older version of salmon (v0.10.1) does not yield this error and quantification progresses successf ...
written 4 weeks ago by bdy850
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Comment: C: Salmon BAM target length different to FASTA file sequence length
... An update, running with no prefiltering (BBduk poly a tail trimming and quality trimming) but still using star alignment causes the same problem. I am now running using only salmon (indexing the genome using gffread, and then salmon index) and then the subsequent salmon quant with the index. ...
written 4 weeks ago by bdy850
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Comment: C: Salmon BAM target length different to FASTA file sequence length
... Hi GenoMax, how I was taking the error was BAM file (-a in salmon) = 536, and the FASTA file (-t in salmon) has 538 or 537. So my thinking is that something has occurred with the STAR or BBDuk.sh processing to cause it to be shorter length. . I am currently running a STAR alignment of the raw read ( ...
written 4 weeks ago by bdy850
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Salmon BAM target length different to FASTA file sequence length
... Good afternoon :) This is more of a theory question. My general pipeline is BBDuk.sh -> STAR align -> salmon quant. I am using 3' RNA-seq (Lexogen QuantSeq FWD prep). During BBDuk.sh, this does a poly a tail trim, as well as a adapter trim (all happy here). I then align the trimmed reads ...
salmon rna-seq written 4 weeks ago by bdy850
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Answer: A: 3' RNA-seq (Lexogen Quant-seq) Mapping Problems with Salmon
... Hi all Thank you for the help, I'm an idiot. A friend who has had a similar problem with Salmon in the past told me to double check the `-l SR` parameter. Lo and behold after going through the kit specifications i needed `-l SF` for the quantseq FWD (its even in the name). Hopefully if anyone ...
written 3 months ago by bdy850
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Comment: C: 3' RNA-seq (Lexogen Quant-seq) Mapping Problems with Salmon
... Hi genomax, so incorporating --softclip increased it marginally by around half a percent. [2020-11-03 16:43:17.801] [jointLog] [info] Mapping rate = 3.98194% As before, the problem still seems to be the number of mappings and fragments discarded due to alignment score. [2020-11-03 16:43:1 ...
written 3 months ago by bdy850
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Comment: C: 3' RNA-seq (Lexogen Quant-seq) Mapping Problems with Salmon
... Thank you so much for this recommendation. I will run this now and update the answer below as well as in the question above. Re my organism, it is not the best reference but compared to other coral genomes that have been used for 3' RNA-seq it is comparable. The 40% i refer to was just a rough e ...
written 3 months ago by bdy850

Latest awards to bdy8

Scholar 21 days ago, created an answer that has been accepted. For A: 3' RNA-seq (Lexogen Quant-seq) Mapping Problems with Salmon
Scholar 3 months ago, created an answer that has been accepted. For A: 3' RNA-seq (Lexogen Quant-seq) Mapping Problems with Salmon

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