Admin: GenoMax

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GenoMax95k
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Posts by GenoMax

<prev • 16,840 results • page 2 of 1684 • next >
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Comment: C: Salmon BAM target length different to FASTA file sequence length
... @Rob thanks for the reminder. I will delete my comment above which should make this part invisible to normal users. ...
written 20 hours ago by GenoMax95k
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Answer: A: Historical Genbank genome assemblies missing?
... Archived human genome assemblies can be found at this [**NCBI FTP**][1] link. [1]: ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/ ...
written 1 day ago by GenoMax95k
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Comment: C: Star index generation - 'std::bad_alloc' error
... While I am not familiar with this particular scripted way of submitting SLURM jobs but at least it must be running under the scheduler. So next obvious question is what is the size of `/gpfs/ysm/scratch60/polimanti/ag2646/Lawsonreference/genome.fa`? `STAR` may need way more than 100G of RAM if your ...
written 1 day ago by GenoMax95k
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Comment: C: Duplicate reads versus unmapped reads
... Yes. ...
written 1 day ago by GenoMax95k
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Comment: C: Duplicate reads versus unmapped reads
... > Are the unmapped reads the same as duplicate reads? Some undoubtedly are but they are not all likely to be duplicates. SMRT-seq is the full length RNAseq kit correct? Have you taken some of the unmapped reads and blasted them at NCBI to see what they are. Specifically to rule out problem with ...
written 1 day ago by GenoMax95k
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Comment: C: Outputting Unassigned reads from Rsubread featureCounts
... I would suggest using `filterreadsbyname.sh` from BBMap for extracting reads from your original data files. Should be plenty fast and no need for reads-groups etc. ...
written 1 day ago by GenoMax95k
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Comment: C: Creating a non-coding RNA index for STAR
... `bbmap` is available via `conda`. So you should consider using that route next time. ...
written 1 day ago by GenoMax95k
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Comment: C: Creating a non-coding RNA index for STAR
... BBMap has tools that do many other things. You will find these tutorials helpful. https://www.biostars.org/p/483592/ https://www.biostars.org/p/483593/ https://www.biostars.org/p/483594 ...
written 1 day ago by GenoMax95k
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Comment: C: Star index generation - 'std::bad_alloc' error
... Based on your original post it is hard to figure out how you are running this job. What scheduler are you using? ...
written 1 day ago by GenoMax95k
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Comment: C: NCBI Eutils error forwarding request
... If you noticed the fasta headers in case of protein database searches they are different as compared to IPG searches. I have clarified that in my comment above. Searches using Entrezdirect did not fail for me as shown by examples above. ...
written 1 day ago by GenoMax95k

Latest awards to GenoMax

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Scholar 7 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Scholar 9 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: how to combine RNA seq data from 4 lanes
Appreciated 9 days ago, created a post with more than 5 votes. For Inviting NEW Biostars moderators to join Biostars slack channel
Scholar 11 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For C: How to analyze Illumina RNASeq data
Scholar 13 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Scholar 13 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: Bowtie2 and hisat2 indexes
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Scholar 14 days ago, created an answer that has been accepted. For A: Error: No Space left on device
Scholar 14 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Appreciated 15 days ago, created a post with more than 5 votes. For Inviting NEW Biostars moderators to join Biostars slack channel
Appreciated 15 days ago, created a post with more than 5 votes. For Inviting NEW Biostars moderators to join Biostars slack channel
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Scholar 16 days ago, created an answer that has been accepted. For A: Error: No Space left on device
Scholar 16 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Commentator 20 days ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
Scholar 20 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen

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