User: ale_abd

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ale_abd30
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Posts by ale_abd

<prev • 8 results • page 1 of 1 • next >
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Answer: A: How to extract a fasta sequence from a batch of multiple fasta genome files
... Supposing you have all your fasta files in the same directory and that they are not linearized (sequence in more than one line): cat *.fasta | awk 'NR==1 {print ; next} {printf /^>/ ? "\n"$0"\n" : $1} END {printf "\n"}' | grep -A1 ACC > ACC.fasta With cat you concatente all the files, th ...
written 3 months ago by ale_abd30
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Comment: C: Question about the type of SRA data (SRR9713131, single- or pair-end?)
... Hi, I agree with you, In the sample that you have mentioned, there are three files. Although you can find other runs from the same project with only two files, sometimes this third file is or unpaired data or it can also be the index (some old related posts: [here][1] and [here][2]). If you see the ...
written 5 months ago by ale_abd30
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Answer: A: Question about the type of SRA data (SRR9713131, single- or pair-end?)
... Hello, SRA stores paired end data on one single *.sra* file, thus, when you download them via SRA files you have to specify that you want the reads to be split: fastq-dump --split-files SRR9713131 If you see this [link][1] ("Data access" tab), you can also see that the uploaded raw data is p ...
written 5 months ago by ale_abd30
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Answer: A: open Reading Frame Prediction
... Hello, As far as I know, you cant use CD-HIT for such purpose. For ORF prediction I can suggest [Prodigal][1] or [FragGeneScan][2] both if you are working with prokaryotes. For Eukaryotic ORFs [Glimmer HMM][3] can be an option. Good luck! [1]: https://github.com/hyattpd/Prodigal [2]: https: ...
written 5 months ago by ale_abd30
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Answer: A: Snakemake wildcards: Not all output, log and benchmark files of rule sortBAM_bbb
... I think your error is on how you are running snakemake (how are you calling the target rule). In my case, I reproduce your first rule and it works! *Snakefile:* rule sortBAM_bbb: input: inBAM = '{PATH}/{sample}.bam' output: outBAM = '{PATH}/{sample}.biob ...
written 5 months ago by ale_abd30
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Comment: C: BLAST Database error: Error pre-fetching sequence data
... Do you have the error while making a blastn search? maybe the problem is with your query sequences rather than with your database ;) ...
written 5 months ago by ale_abd30
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Answer: A: I want to use droptag but I don't have the barcodes in .fastq format, they're in
... Hello, I'm not sure how droptag works, but maybe you can use QIIME's [extract_barcodes.py][1] script, this script will separate your fastq files into barcodes (fastq format) and sequences. Then you can just use also QIIME's [split_libraries_fastq.py][2] to demultiplex your files or give it a try to ...
written 5 months ago by ale_abd30
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Answer: A: How to make a custom blast db with taxon IDs from a taxid_map file
... Is important to bear in mind that makeblastdb command parse fasta sequence ids as >ACC.version, but it seems that the taxid_map option parses the taxid map without taking into account the same format *ACC.version*, therefore if you want to build a blast database with sequence that looks like: ...
written 5 months ago by ale_abd30

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