Update README.md

jlanga · Jul 18, 2019 · c1d0eef · c1d0eef
1 parent 33e300a
commit c1d0eef
Showing 1 changed file with 60 additions and 70 deletions.
diff --git a/README.md b/README.md
@@ -5,63 +5,38 @@
 Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
 
 ## Requirements
-```
-abyss==2.0.1  (something is happening with 2.0.2 and abyss-bloom kmers)
-bedtools (tested on 2.0)
-python3
-biopython
-networkx
-pandas
-biobloomtools
-```
-We recomend installing these packages with `conda` and `bioconda`
-
-## How to install
 
-Copy this repo and install it with `pip`:
+Docker or different apt and conda packages (see installation guide).
 
-```sh
-git clone https://github.com/jlanga/exfi.git
-pip install --user exfi
-```
+## How to install
 
 To install other dependencies, follow the instructions from the travis files:
 
 1. Install packages with `apt`:
 
 ```sh
-sudo apt install build-essential git curl libboost-dev gcc autoconf bzip2 zlib1g libsparsehash-dev
+sudo apt install \
+    autoconf build-essential bzip2 cmake curl gcc git libboost-dev libsdsl3 \
+    libz-dev zlib1g
 ```
 
-2. Install conda, then
+2. Install conda, then configure channels and install
 
 ```sh
 conda config --add channels conda-forge
 conda config --add channels defaults
 conda config --add channels r
 conda config --add channels bioconda
-conda install --yes abyss biopython bedtools networkx pandas pip
+conda install --yes abyss=2.0.1 bedtools biopython pandas pip
 ```
 
 3. Install `biobloomtools`
 
-There is an easy way, with `brew` (not the latest release):
-
-```sh
-brew install biobloomtools
-```
-
-Or the manual way:
+You may need to use `sudo`:
 
 ```sh
-# Install SDSL-Lite
-git clone https://github.com/simongog/sdsl-lite.git
-pushd sdsl-lite/ && \
-sudo ./install.sh /usr/local/ && \
-popd
-
 # Install biobloomtools
-git clone https://github.com/bcgsc/biobloom.git
+git clone --recursive https://github.com/bcgsc/biobloom.git
 pushd biobloom/ && \
 git submodule update --init && \
 ./autogen.sh && \
@@ -71,6 +46,21 @@ sudo make install && \
 popd
 ```
 
+4. Copy this repo and install it with `pip`:
+
+```sh
+git clone --recursive https://github.com/jlanga/exfi.git
+pip install --user exfi
+```
+
+If you have access to Docker, you can create a Debian container with the following command:
+
+```sh
+docker build --rm --tag exfi:v1.5.6 github.com/jlanga/exfi-docker
+```
+
+[More info](https://github.com/jlanga/exfi-docker)
+
 
 
 ## Required data
@@ -83,30 +73,31 @@ popd
 
 1. Make a baited Bloom filter of the genomic reads with `build_baited_bloom_filter`:
 - `genome.fa.gz` is the set of genomic reads and
-- `genome_k27_m500M_l1.bloom` is the resulting Bloom filter, made of kmers of length 27, a size of 500 Mb and the number of times of a kmer must be in the reads is 1 (levels).
+- `genome_k25_m100M_l1.bf` is the resulting Bloom filter, made of kmers of length 25, a size of 100 MB and the number of times of a kmer must be in the reads is 1 (levels).
 
 ```sh
+# Assuming that you are in the exfi folder:
 build_baited_bloom_filter \
     --input-fasta data/transcript.fa \
-    --kmer 27 \
-    --bloom-size 500M \
+    --kmer 25 \
+    --bloom-size 100M \
     --levels 1 \
     --threads 4 \
-    --output-bloom results/genome_k27_m500M_l1.bloom \
+    --output-bloom results/genome_k25_m100M_l1.bf \
     genome.fa.gz
 ```
 
 2. Run `build_splice_graph` to get putative exons in the transcriptome.
 - `data/transcript.fa` is the input transcriptome,
-- `genome_k27_m500M_l1.bloom` is the Bloom filter generated above
+- `genome_k25_m500M_l1.bf` is the Bloom filter generated above
 - kmer length has to be the same
 - `test.gfa` is the resulting splice graph in [GFA1 format](https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md).
 
 ```sh
 build_splicegraph \
     --input-fasta data/transcript.fa \
-    --input-bloom results/genome_k27_m500M_l1.bloom \
-    --kmer 27 \
+    --input-bloom results/genome_k25_m100M_l1.bloom \
+    --kmer 25 \
     --max-fp-bases 5 \
     --output-gfa test.gfa
 ```
@@ -116,35 +107,34 @@ This splice graph can be visualized with [Bandage](https://rrwick.github.io/Band
 Example:
 
 ```
-H       VN:Z:1.0
-S       EXON00000000001 GTAAGCCGCGGCGGTGTGTGTGTGTGTGTGTGTTCTCCGTCATCTGTGTTCTGCTGAATGATGAGGACAGACGTGTTTCTCCAGCGGAGGAAGCGTAGAGATGTTCTGCTCTCCATCATCGCTCTTCTTCTGCTCATCTTCGCCATCGTTCATCTCGTCTTCTGCGCTGGACTGAGTTTCCAGGGTTCGAGTTCTGCTCGCGTCCGCCGAGACCTC        LN:i:216
-S       EXON00000000002 GAGAATGCGAGTGAGTGTGTGCAGCCACAGTCGTCTGAGTTTCCTGAAGGATTCTTCACGGTGCAGGAGAGGAAAGATGGAGGAATCCTGATTTACTTCATGATCATCTTCTACATGCTGCTGTCCGTCTCCATCGTGTGTGATGAATATTTTCTGCCATCTCTGGAGGTCATCAGCGAGCG  LN:i:182
-S       EXON00000000003 GTCTTGGTCTCTCGCAGGATGTTGCTGGAGCCACGTTTATGGCTGCGGGGAGTTCGGCTCCAGAGCTCGTCACTGCATTTCTGGG   LN:i:85
-S       EXON00000000004 GGTGTGTTTGTGACGAAGGGCGACATCGGCGTCAGCACCATCATGGGTTCTGCTGTCTATAACCTGCTGTGCATCTGTGCAGCGTGCGGCCTGCTGTCCTCTGCAG      LN:i:106
-S       EXON00000000005 GTTGGTCGTCTGAGCTGCTGGCCGTTGTTCAGAGATTGTGTTGCGTACTCCATCAGTGTCGCCGCCGTCATCGCCATCATCTCAGATAACAGAGTTTACTGG  LN:i:102
-S       EXON00000000006 GGTATGATGGCGCGTGTCTCCTGCTGGTGTACGGTGTGTATGTAGCTGTACTGTGTTTCGATCTGAAGATCAGCGAGTACGTGATGCAGCGCTTCAGTCCATGCTGCTGGTGTCTGAAACCTCGCGATCGTGACTCAGGCGAGCAGCAGCCTCTAGTGGGCTGGAGTGACGACAGCAGCCTGCGGGTCCAGCGCCGTTCCAGAAATGACAGCGGAATATTCCAGGATGATTCTGGATATTCACATCTATCGCTCAGCCTGCACGGACTCAACGAAATCAGCGAC    LN:i:284
-S       EXON00000000007 GAGCACAAGAGTGTGTTCTCCATGCCGGATCACGATCTGAAGCGAATCCTGTGGGTTTTGTCTCTTCCGGTCAGCACTCTGCTGTTTGTGAGCGTTCCCGACTGCAGGAGACCCTTCTGGAAGAACTTCTACATGCTGACCTTCCTGATGTCCGCCGTCTGGATTTCTGCATTCACTTATGTGCTGGTCTGGATGGTCACAATCGTGG        LN:i:208
-S       EXON00000000008 GGGGAGACTCTGGGAATCCCGGACACAGTGATGGGAATGACTCTTCTGGCTGCAGGAACCAGTATCCCCGACACCGTGGCCAGTGTGATGGTGGCACGAGAAGGTAA     LN:i:107
-S       EXON00000000009 AGGTAAATCTGATATGGCCATGTCCAACATCGTGGGCTCTAACGTGTTCGATATGCTGTGTCTGGGCCTGCCGTGGTTCATCCAGACGGTGTTTGTTGACGTGGGCTCCCCGGTGGATGTCAACAGCTCGGGGCTGGTCTTCATGTCCTGCACGCTGCTGCTCTCCATCATCTTCCTCTTCCTCGCCGTGCACATCAACGGCTGGAAGCTGGACTGGAAGCTGGGTCTGGTGTGTTTGGCGTGTTACATTCTGTTCGCAACACTCTCCATCCTGTACGAGCTCGGCATCATCGGGAACAATCCCATACGCTCCTGCAGCGACTGAACACTGCTCTACAGCGCCCCCTTATGGACAACACAAGGACGTGACTCTTTATAACCCTCTAAAGTGCACAGGTTCATTACTGAATACAAGAAAATAGAACTGCGAGACGTCAACTCAAAATACAAGAGAAGTCAAAGTGCGAGATGTAAAAAATATATGCACATAAATGAGGATAAACTTTTTATTTAATAAGACAAAACTGCATAAAGTCTGATGTGAACACTGCTCAACAGCGCCCTCTCATGGACAACACATGGATCTGACTCTTATTAACCCTCCAGAGTGCAAATACACTAACACAACGTAATATAACCAAGTTAAAATGGCAAGATGTGAACTCAAAATACAAGAAAGCAGTCAAGATGCCCGACATAACAAATGTGCATTAAAATGTAAGCCC   LN:i:725
-L       EXON00000000001 +       EXON00000000002 +       0M
-L       EXON00000000002 +       EXON00000000003 +       1M
-L       EXON00000000003 +       EXON00000000004 +       2M
-L       EXON00000000004 +       EXON00000000005 +       1M
-L       EXON00000000005 +       EXON00000000006 +       2M
-L       EXON00000000006 +       EXON00000000007 +       0M
-L       EXON00000000007 +       EXON00000000008 +       1M
-L       EXON00000000008 +       EXON00000000009 +       6M
-C       ENSDART00000033574.5    +       EXON00000000001 +       0       216M
-C       ENSDART00000033574.5    +       EXON00000000002 +       216     182M
-C       ENSDART00000033574.5    +       EXON00000000003 +       397     85M
-C       ENSDART00000033574.5    +       EXON00000000004 +       480     106M
-C       ENSDART00000033574.5    +       EXON00000000005 +       585     102M
-C       ENSDART00000033574.5    +       EXON00000000006 +       685     284M
-C       ENSDART00000033574.5    +       EXON00000000007 +       969     208M
-C       ENSDART00000033574.5    +       EXON00000000008 +       1176    107M
-C       ENSDART00000033574.5    +       EXON00000000009 +       1277    725M
-P       ENSDART00000033574.5    EXON00000000001+,EXON00000000002+,EXON00000000003+,EXON00000000004+,EXON00000000005+,EXON00000000006+,EXON00000000007+,EXON00000000008+,EXON00000000009+
-
+H	VN:Z:1.0
+S	ENSDART00000033574.5:0-216	GTAAGCCGCGGCGGTGTGTGTGTGTGTGTGTGTTCTCCGTCATCTGTGTTCTGCTGAATGATGAGGACAGACGTGTTTCTCCAGCGGAGGAAGCGTAGAGATGTTCTGCTCTCCATCATCGCTCTTCTTCTGCTCATCTTCGCCATCGTTCATCTCGTCTTCTGCGCTGGACTGAGTTTCCAGGGTTCGAGTTCTGCTCGCGTCCGCCGAGACCTC
+S	ENSDART00000033574.5:216-398	GAGAATGCGAGTGAGTGTGTGCAGCCACAGTCGTCTGAGTTTCCTGAAGGATTCTTCACGGTGCAGGAGAGGAAAGATGGAGGAATCCTGATTTACTTCATGATCATCTTCTACATGCTGCTGTCCGTCTCCATCGTGTGTGATGAATATTTTCTGCCATCTCTGGAGGTCATCAGCGAGCG
+S	ENSDART00000033574.5:397-482	GTCTTGGTCTCTCGCAGGATGTTGCTGGAGCCACGTTTATGGCTGCGGGGAGTTCGGCTCCAGAGCTCGTCACTGCATTTCTGGG
+S	ENSDART00000033574.5:480-586	GGTGTGTTTGTGACGAAGGGCGACATCGGCGTCAGCACCATCATGGGTTCTGCTGTCTATAACCTGCTGTGCATCTGTGCAGCGTGCGGCCTGCTGTCCTCTGCAG
+S	ENSDART00000033574.5:585-687	GTTGGTCGTCTGAGCTGCTGGCCGTTGTTCAGAGATTGTGTTGCGTACTCCATCAGTGTCGCCGCCGTCATCGCCATCATCTCAGATAACAGAGTTTACTGG
+S	ENSDART00000033574.5:685-969	GGTATGATGGCGCGTGTCTCCTGCTGGTGTACGGTGTGTATGTAGCTGTACTGTGTTTCGATCTGAAGATCAGCGAGTACGTGATGCAGCGCTTCAGTCCATGCTGCTGGTGTCTGAAACCTCGCGATCGTGACTCAGGCGAGCAGCAGCCTCTAGTGGGCTGGAGTGACGACAGCAGCCTGCGGGTCCAGCGCCGTTCCAGAAATGACAGCGGAATATTCCAGGATGATTCTGGATATTCACATCTATCGCTCAGCCTGCACGGACTCAACGAAATCAGCGAC
+S	ENSDART00000033574.5:969-1177	GAGCACAAGAGTGTGTTCTCCATGCCGGATCACGATCTGAAGCGAATCCTGTGGGTTTTGTCTCTTCCGGTCAGCACTCTGCTGTTTGTGAGCGTTCCCGACTGCAGGAGACCCTTCTGGAAGAACTTCTACATGCTGACCTTCCTGATGTCCGCCGTCTGGATTTCTGCATTCACTTATGTGCTGGTCTGGATGGTCACAATCGTGG
+S	ENSDART00000033574.5:1176-1283	GGGGAGACTCTGGGAATCCCGGACACAGTGATGGGAATGACTCTTCTGGCTGCAGGAACCAGTATCCCCGACACCGTGGCCAGTGTGATGGTGGCACGAGAAGGTAA
+S	ENSDART00000033574.5:1277-2002	AGGTAAATCTGATATGGCCATGTCCAACATCGTGGGCTCTAACGTGTTCGATATGCTGTGTCTGGGCCTGCCGTGGTTCATCCAGACGGTGTTTGTTGACGTGGGCTCCCCGGTGGATGTCAACAGCTCGGGGCTGGTCTTCATGTCCTGCACGCTGCTGCTCTCCATCATCTTCCTCTTCCTCGCCGTGCACATCAACGGCTGGAAGCTGGACTGGAAGCTGGGTCTGGTGTGTTTGGCGTGTTACATTCTGTTCGCAACACTCTCCATCCTGTACGAGCTCGGCATCATCGGGAACAATCCCATACGCTCCTGCAGCGACTGAACACTGCTCTACAGCGCCCCCTTATGGACAACACAAGGACGTGACTCTTTATAACCCTCTAAAGTGCACAGGTTCATTACTGAATACAAGAAAATAGAACTGCGAGACGTCAACTCAAAATACAAGAGAAGTCAAAGTGCGAGATGTAAAAAATATATGCACATAAATGAGGATAAACTTTTTATTTAATAAGACAAAACTGCATAAAGTCTGATGTGAACACTGCTCAACAGCGCCCTCTCATGGACAACACATGGATCTGACTCTTATTAACCCTCCAGAGTGCAAATACACTAACACAACGTAATATAACCAAGTTAAAATGGCAAGATGTGAACTCAAAATACAAGAAAGCAGTCAAGATGCCCGACATAACAAATGTGCATTAAAATGTAAGCCC
+L	ENSDART00000033574.5:0-216	+	ENSDART00000033574.5:216-398	+	0M
+L	ENSDART00000033574.5:216-398	+	ENSDART00000033574.5:397-482	+	1M
+L	ENSDART00000033574.5:397-482	+	ENSDART00000033574.5:480-586	+	2M
+L	ENSDART00000033574.5:480-586	+	ENSDART00000033574.5:585-687	+	1M
+L	ENSDART00000033574.5:585-687	+	ENSDART00000033574.5:685-969	+	2M
+L	ENSDART00000033574.5:685-969	+	ENSDART00000033574.5:969-1177	+	0M
+L	ENSDART00000033574.5:969-1177	+	ENSDART00000033574.5:1176-1283	+	1M
+L	ENSDART00000033574.5:1176-1283	+	ENSDART00000033574.5:1277-2002	+	6M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:0-216	+	0	216M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:216-398	+	216	182M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:397-482	+	397	85M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:480-586	+	480	106M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:585-687	+	585	102M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:685-969	+	685	284M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:969-1177	+	969	208M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:1176-1283	+	1176	107M
+C	ENSDART00000033574.5	+	ENSDART00000033574.5:1277-2002	+	1277	725M
+P	ENSDART00000033574.5	ENSDART00000033574.5:0-216+,ENSDART00000033574.5:216-398+,ENSDART00000033574.5:397-482+,ENSDART00000033574.5:480-586+,ENSDART00000033574.5:585-687+,ENSDART00000033574.5:685-969+,ENSDART00000033574.5:969-1177+,ENSDART00000033574.5:1176-1283+,ENSDART00000033574.5:1277-2002+	*
 ```
 
 3.  Get exonic sequences