User: amy_houseman

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Posts by amy_houseman

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Comment: A: subread keeps makes a weird .sam file, have i done something wrong?
... Hi, So after installing samtools and doing the above command, I get [this result:][1] ![samtools view][2] I haven't changed the .sam to a .bam file yet, so I'll await your response till I do so. Thanks for all your help. Amy [1]: https://1drv.ms/u/s!ArwhyLzdnOxrguh4sLOe8fi4y-tDsg?e=J1Azvv ...
written 19 days ago by amy_houseman0
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Comment: C: subread keeps makes a weird .sam file, have i done something wrong?
... Hi! The result of file my_results.sam is this: (which also doesn't look very promising): `my_results.sam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 246` Thanks again ...
written 20 days ago by amy_houseman0
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subread keeps makes a weird .sam file, have i done something wrong?
... Hi all, I have DNA Sanger sequence FASTA files from patient TGM1 genes, and have been trying to use subread to align them to the TGM1 coding reference sequence from [NCBI][1]. I keep getting a weird red looking .sam file as the result from the alignment but it doesn't look correct at all. I've a ...
subread alignment rsubread reference dna written 20 days ago by amy_houseman0
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... I have some DNA nucleotide sequences from exons in TGM1 gene of people with disease, so I'm trying to align them to the reference coding sequence of TGM1, and then hopefully find the variants and then use another tool after to find the pathogenicity of each variant? If that makes sense. Do you kno ...
written 20 days ago by amy_houseman0
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Hi, I made that change but it still doesn't seem to work, the command does seem to create 5 file types but they end up in the `fasta_reference_TGM1_folder`. If I manually move these files into the `TGM1_index` file and then run: `subread-align -T 1 -i /home/amyhouseman/Desktop/fasta_reference_T ...
written 20 days ago by amy_houseman0
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Hi! The return for that is: -rw-rw-r-- 1 amyhouseman amyhouseman 0 Feb 9 12:51 /home/amyhouseman/Desktop/fasta_reference_TGM1_folder/TGM1_index The process I did to get to this point was: > 1. Installed subread from the website: http://bioinf.wehi.edu.au/subread-package/ > 2. sudo apt ...
written 21 days ago by amy_houseman0 • updated 21 days ago by GenoMax96k
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Its around 2,453bp (its the coding seq for https://www.ncbi.nlm.nih.gov/nuccore/NM_000359.3). I think my laptop may only be 8GB of RAM as I think its this one: https://www.laptopsdirect.co.uk/lenovo-v15-ada-amd-ryzen-3-3250u-8gb-256gb-ssd-15.6-inch-fhd-windows-10-lap-82c70004uk/version.asp Sorry ...
written 22 days ago by amy_houseman0
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Hi, I'm not sure, when I go to settings it says: Memory 5.7GiB.. Disk capacity 256.1GB. Although, I did dual boot the laptop so it has both windows and Ubuntu. So that might not be helping? Thanks! ...
written 22 days ago by amy_houseman0
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... ah yes! Such a simple error, thank you! However, now it says 'Segmentation fault (core dumped)' - which I assume is a memory error? But I checked the system monitor and I'm only using 20% - Thanks for your help, I really appreciate it ...
written 22 days ago by amy_houseman0
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Hi, thanks for your reply. I meant this is the code I entered (please excuse my messy files): subread-align -i home/amyhouseman/Desktop/fasta_reference_TGM1_folder/TGM1_index -r /home/amyhouseman/Desktop/katja_fasta_seq/fasta_trimmed_sequences/fasta_trimmed_1_all/fasta_trimmed_1_final -t 1 -o ...
written 22 days ago by amy_houseman0 • updated 22 days ago by GenoMax96k

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