User: mnmalash

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mnmalash0
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Posts by mnmalash

<prev • 13 results • page 1 of 2 • next >
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CD-hit records matching and parsing
... I have a CD-hit result file (for who is familiar with CD-hit). I want to paste the second column value from another file which is a 2-column tab delimited table into the CD-hit file next to the respective matching RUN ID (like that highlighted with green in the sample image). RUN ID is the 1st colum ...
python cd-hit text processing bioinformatics bash written 5 months ago by mnmalash0
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Comment: C: Downloading individual reads from SRA
... It worked well with single ends and paired ends. However, in paired ends, it downloads both not either of them alone. '-N' and '-X' options do not accept other than numerals. They do not accept the dot (.1 or .2) do you have a way to download either of them when wanted? ...
written 7 months ago by mnmalash0
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Comment: C: Downloading individual reads from SRA
... I have already searched the whole sequences for HMMs of interest and those are the positive reads and their IDs are in the report. I want them separately. ...
written 7 months ago by mnmalash0
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Comment: C: Downloading individual reads from SRA
... perfect. This is what I want. I will go for this and see what I will get and will try it for paired end reads and tell you. I will work on both. ...
written 7 months ago by mnmalash0
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Comment: C: Downloading individual reads from SRA
... I mean downloading individual reads I know their IDs just like this for example SRR123456.4564 and don't want to download the whole SRR123456 run file which may be large and will take time. Provided I want a list of reads from many SRA runs. ...
written 7 months ago by mnmalash0
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Downloading individual reads from SRA
... How can I download selected individual reads from SRA without downloading the whole run file using command line? ...
gene sequence next-gen sequencing written 7 months ago by mnmalash0 • updated 7 months ago by vkkodali1.1k
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Comment: C: 454 and illumina adapters
... Thanks @genomax for your great answer. It worked well for illumina sequences but for 454, most of the reads were eliminated after trimming due to size control by skewer (which is 30 bp). should I use the 454 adapters list? or just use the illumina one as they are shorter reads? ...
written 14 months ago by mnmalash0
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454 and illumina adapters
... Is there a universal list of 454 and illumina adapters? so that I can trim them using *skewer* other than its default which misses others. I am working on multiple sequences (454 and illumina) retrieved from SRA. ...
next-gen sequencing written 14 months ago by mnmalash0
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Comment: C: fastx_clipper problem in output
... this is awesome. Thank you dear ...
written 15 months ago by mnmalash0
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Comment: C: fastx_clipper problem in output
... Thanks for the nice recommendations. I have read about *skewer* as you recommended and I see it makes quality filtering. Does this mean I don't need quality filtering by other methods such as *pearf* or even *fastq_quality_filter* of fastx-toolkit and it will do both functions at once? ...
written 15 months ago by mnmalash0

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