User: Sammy

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Sammy10
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3 months, 1 week ago
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1 year, 2 months ago
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Posts by Sammy

<prev • 28 results • page 1 of 3 • next >
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HISAT2 on multiple samples
... Hey, I am using HISAT2 to align publicly available data. I have around 100 samples of paired-end reads. hisat2 -p 8 -x refgenome --sra-acc SRRxxxxxxx,SRRxxxxxxx,SRRxxxxxxx But I am not sure how to manage the output. I tried `-S out1_file.bam out2_file.bam out3_file.bam` but it doesn't seem ...
rna-seq written 3 months ago by Sammy10 • updated 3 months ago by swbarnes27.8k
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Trimming Adapters for RNA-SEQ (Quality Check)
... Heyya, I am processing publicly available SRA. I developed the pipeline, however I skipped the FASTQC step so I have to go back. I tried to figure out a quick way to do it. Correct me if I am wrong: Processing publicly available data has some downsides: you don't know loads of things about the RNA ...
rna-seq written 5 months ago by Sammy10 • updated 5 months ago by jrleary110
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Comment: C: Multiple Sequence Alignment viewers or How to Build a Conservation Plot
... It worked with conda afterall. ...
written 7 months ago by Sammy10
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Comment: C: Multiple Sequence Alignment viewers or How to Build a Conservation Plot
... Cheers! Actually I am trying to get started with Jalview right now. It is installed. The newest version 2.11.0. The pink Launch Button from the side is missing. Instead it says to get an installer. I got the installer (I think): Offline Unix shell installer. I cannot find any instructions. I still c ...
written 7 months ago by Sammy10
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Comment: C: Multiple Sequence Alignment viewers or How to Build a Conservation Plot
... Basically, pretty colours for a PPT. So the conserved region will be obvious for everyone. ...
written 7 months ago by Sammy10
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Comment: C: Multiple Sequence Alignment viewers or How to Build a Conservation Plot
... Yest. I meant fasta. Thank you. ...
written 7 months ago by Sammy10
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Multiple Sequence Alignment viewers or How to Build a Conservation Plot
... Hey, I want to get a Conservation Plot across 4 - 5 species. I researched Multiple Sequence Alignment viewers and I encounterd eShadow, zPicture and SeqTools (Belvu). I got different results from eShadow and zPicture (or I have difficulties putting together the results). I am preparing to install Se ...
rna-seq written 7 months ago by Sammy10 • updated 7 months ago by h.mon29k
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Comment: C: Orientation of PE reads a review of --fr --ff and --rf meanings
... I posted an update of the picture. I added the sequencing arrows. I have one question. I noticed that the library types from rf explanation are different in our drawings. Your rf-firststrand (I used reverse (from HISAT) same thing) has the read that corresponds to the second strand (original RNA d ...
written 9 months ago by Sammy10
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Answer: A: Orientation of PE reads a review of --fr --ff and --rf meanings
... Here is my interpretation of the library types and relative orientation of the reads. I hope that the image is self-explanatory. FF library is tricky. IMPORTANT NOTE: I know that rr is not technically correct and is basically the same thing as ff. However it helped to make my point clearer ![Librar ...
written 9 months ago by Sammy10
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Comment: C: Orientation of PE reads a review of --fr --ff and --rf meanings
... Sorry that the image has such a bad quality. Did not expect that. ...
written 9 months ago by Sammy10

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