User: syrez.m

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syrez.m0
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Posts by syrez.m

<prev • 8 results • page 1 of 1 • next >
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Commandline Bowtie2 and variant call help.
... Hello there! When you run bowtie2 to align the reads to the genome, some stats about the file are displayed: xxxxxx reads; of these:   nnnnnn (f%) were unpaired; of these:     aaaaaa (g%) aligned 0 times     bbbbbb (h%) aligned exactly 1 time     cccccc (j%) aligned >1 times Can you say 'n ...
samtools mpileup bowtie variantcall written 2.2 years ago by syrez.m0 • updated 2.2 years ago by Jennifer Hillman Jackson23k
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Comment: C: Bowtie-build : Finding information from bowtie2 indexed genome file
... thanks Jen! I am using command line tools and prompt% was not found so I edited it to be cat genome.fas | grep ">" | sed 's/^>//' | cut -f1 | more  I have a feeling that it worked because it displayed the following output: Chr1 Chr2 Chr3 Chr4 Chr5 chloroplast mitochondria     ...
written 2.2 years ago by syrez.m0
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Bowtie-build : Finding information from bowtie2 indexed genome file
... Hi all! I did a bowtie2 index on a genome file using bowtie2-build. How do I find the following information? Number of sequences in the genome?  Name(s) of the sequence in the genome file?  Thanks! ...
bowtie written 2.2 years ago by syrez.m0 • updated 2.2 years ago by Jennifer Hillman Jackson23k
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Comment: C: A question of concept?
... Thanks Jennifer! ...
written 2.2 years ago by syrez.m0
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A question of concept?
... Hi all! I'm new to this so, pardon my noobness. If I were to convert the transcript annotations from a GTF into BED format, how many BED records would be generated? Would it be equal to total number of transcripts in the GTF file? One BED record for each transcript?   Thanks! ...
records gtf bed written 2.2 years ago by syrez.m0 • updated 2.2 years ago by Jennifer Hillman Jackson23k
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Commandline SAMtools/BEDtools help!
... Hi all!  I'm trying to teach myself SAMtools/bedtools commands (on UNIX running on a VM). For practice, I have found a .bam file. I'm trying to find an online source which will show me how to do the following. How many alignments does the set contain? How many alignments show the read’s mate unma ...
samtools flagstat command line bedtools written 2.2 years ago by syrez.m0 • updated 2.2 years ago by Jennifer Hillman Jackson23k
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Answer: A: Running Filter on BAM file
... Nevermind, I realized there is a specific Filter BAM datasets on a variety of attributes (Galaxy Tool Version 0.0.1) ...
written 2.2 years ago by syrez.m0
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Running Filter on BAM file
... I'm trying to run Filter on a MergeSamFile output dataset which is in BAM format.  Filter (Galaxy Tool Version 1.1.0) can not detect any applicable dataset to run and is looking for a 'Tabular dataset' in my history. What am I doing wrong? Please advice! Thanks! ...
bam filter mergesamfile written 2.2 years ago by syrez.m0

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