User: mastal511

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Posts by mastal511

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Comment: C: Problem for finding "Locus Link ID" from Annotation file
... NCBI's LocusLink became Entrez Gene sometime around 2004. 'gene_id' would probably be closest, unless the software you are using actually expects the old LocusLink numbers. ...
written 13 months ago by mastal5112.0k
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Comment: C: Trimmomatic: Higher number of "forward only" than "reverse only" surviving reads
... See this previouis discussion about Trimmomatic. https://www.biostars.org/p/325174/#325193 By default, trimmomatic deletes the reverse read when it trims adapters from paired reads, leaving an excess of unpaired forward reads. ...
written 13 months ago by mastal5112.0k
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Comment: C: Parsing a FASTQ File
... Qiime1 has a script, split_sequence_file_on_sample_ids.py, which will separate fastq or fasta files demultiplexed using split_libraries.py, into separate files for each sample. But this will not separate forward reads from reverse reads, if your forward and reverse reads are all in one file. ...
written 14 months ago by mastal5112.0k
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Answer: A: Interpretation of Trimmomatic Results after Paired-End Adapter Trimming
... Trimmomatic's default behaviour is to drop the reverse reads when it trims adapters, so you get forward reads only surviving as a result. The reasoning behind this is that when you read into the adapter sequences it means that the insert is shorter than one of the reads, so the reverse read doesn' ...
written 14 months ago by mastal5112.0k
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Comment: C: bowtie2-build index files missing
... It looks like bowtie-build did not produce all the files for the index, and you are missing the ones mentioned in the error message, so the bowtie-build command did not complete successfully. Since you are working with a large genome, you may need more memory, as already mentioned by Mehmet, segment ...
written 15 months ago by mastal5112.0k
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Comment: C: Low mapping percentage after mapping RNA-seq reads to a closely related species
... I think the first thing to do when you get a very low mapping percentage, is to take some of your reads and do blast against the ncbi nr database, and see what kind of organisms you get hits to. Your reads may not be what you expected them to be. ...
written 15 months ago by mastal5112.0k
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Comment: C: Rarefaction on R
... Have you tried the vegan package in R? You can also do rarefaction with qiime. ...
written 15 months ago by mastal5112.0k
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Comment: C: Trimmomatic Error and Permission Denied
... First, you want to make sure you download the binary version of trimmomatic and not the source version. Then, from the linux command line, you need to unzip the file with the 'unzip' command. The downloaded file needs to be in a directory where you have write permission in order to modify files. ...
written 16 months ago by mastal5112.0k
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Comment: C: QIIME filter_fasta.py not removing chimeric sequences
... Have you had a look at the qiime webpage for the filter_fasta.py command? http://qiime.org/scripts/filter_fasta.html It looks as if the file passed with the -s parameter should just have a list of the IDs of the sequences you want to remove, rather than the actual sequences. Try and see if this he ...
written 16 months ago by mastal5112.0k
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Comment: C: Read length of RNA-seq from HiSeq 2500
... Illumina reads are all the same length, unless someone has trimmed them to remove adapters, low quality bases, etc., which is sometimes done by the sequencing center. ...
written 17 months ago by mastal5112.0k

Latest awards to mastal511

Scholar 14 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Appreciated 15 months ago, created a post with more than 5 votes. For A: Weird fastq format
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: how to plot heat map
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: how to plot heat map
Scholar 2.3 years ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Weird fastq format
Scholar 2.4 years ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
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